} else if (strncmp(buf, " $VEC", 5) == 0) {
Double *coeffs;
/* Read the vec group */
- if (mol->bset == NULL)
+ if (mol->bset == NULL || mol->bset->ncomps == 0)
continue; /* Just ignore */
if (optimizing)
continue; /* Ignore VEC group during optimization */
int MoleculeLoadTepFile(Molecule *mp, const char *fname, char *errbuf, int errbufsize);
int MoleculeLoadShelxFile(Molecule *mp, const char *fname, char *errbuf, int errbufsize);
int MoleculeLoadGaussianFchkFile(Molecule *mp, const char *fname, char *errbuf, int errbufsize);
+int MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char *errbuf, int errbufsize);
Molecule *MoleculeNewWithName(const char *name);
Molecule *MoleculeInitWithAtoms(Molecule *mp, const Atom *atoms, int natoms);
Molecule *MoleculeInitWithMolecule(Molecule *mp2, const Molecule *mp);
register_fragment(formula_name[i], f)
}
register_fragment("Me", known_fragment("CH3"))
+ load(MbsfPath + "/fragment_def.rb")
+ if 0
register_fragment("Ph", fragment_from_dump(%q(
0 BEN.1 C1 ca C -0.653 0.585 -1.068 -0.128 [1,2,10]
1 BEN.1 _1 "" Du -1.158 1.039 -1.898 0.128 [0]
9 BEN.1 _3 "" Du -1.298 -1.077 1.792 0.128 [8]
10 BEN.1 C6 ca C -1.384 -0.021 -0.060 -0.128 [0,8,11]
11 BEN.1 H6 ha H -2.455 -0.038 -0.110 0.128 [10])))
-
+ end
+
# Returns an arbitrary unit vector that is orthogonal to v
def orthogonal_vector(v)
vx = v.cross(Vector3D[1, 0, 0])
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CBT C1 c3 -0.00353 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CBT H11 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CBT H12 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CBT C2 c3 -0.00353 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CBT H21 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CBT H22 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CBT C3 c3 -0.00353 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CBT H31 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CBT H32 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 CBT C4 c3 -0.00353 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 CBT H41 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 CBT H42 hc 0.00177 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 0.09510873 0.42296547 0.67454986
+1 -0.29829705 1.02543431 -0.13627522
+2 -0.73590500 -0.09659789 1.13784696
+3 1.28583734 -0.48684553 0.28229631
+4 1.58569435 -0.41414050 -0.75692159
+5 1.14813096 -1.53613494 0.51724917
+6 2.19806792 0.28061820 1.27138096
+7 3.02903956 0.80021029 0.80804053
+8 2.59153544 -0.32182896 2.08219215
+9 1.00732651 1.19039636 1.66367180
+10 1.14501616 2.23970199 1.42878169
+11 0.70746654 1.11762469 2.70288420
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 9 11
+9 10 6 9 0 3 0 9
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 11 9 10 8 6 9
+7 6 9 3 6 9 6 9 11
+6 9 10 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+1 0 9 2 0 9 3 0 9
+0 9 11 0 9 10 0 9 6
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+8 6 9 11 8 6 9 10
+7 6 9 11 7 6 9 10
+3 6 9 11 3 6 9 10
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+5 3 6 9 4 3 6 9
+0 3 6 8 0 3 6 7
+0 3 6 9 1 0 9 11
+1 0 9 10 1 0 9 6
+2 0 9 11 2 0 9 10
+2 0 9 6 3 0 9 11
+3 0 9 10 3 0 9 6
+9 0 3 5 9 0 3 4
+9 0 3 6 8 6 9 0
+7 6 9 0 3 6 9 0
+
+!:md_parameters
+log_file cyclopentane.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 135
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+103.570824 -0.936221 0.190556 -0.295260
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CHP C1 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CHP H11 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CHP H12 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CHP C2 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CHP H21 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CHP H22 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CHP C3 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CHP H31 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CHP H32 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 CHP C4 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 CHP H41 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 CHP H42 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 CHP C5 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 CHP H51 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 CHP H52 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+15 MAIN 1 CHP C6 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+16 MAIN 1 CHP H61 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+17 MAIN 1 CHP H62 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+18 MAIN 1 CHP C7 c3 0.01843 12.01070 C 6 1.000000 0.000000 0
+19 MAIN 1 CHP H71 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+20 MAIN 1 CHP H72 hc -0.00921 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.96277556 1.22723393 1.99218760
+1 -0.51859032 0.55324938 2.72097554
+2 -1.74879231 1.75559255 2.52526798
+3 0.08120907 2.26711992 1.55221334
+4 0.66512402 2.54158972 2.42755275
+5 -0.43139542 3.17477837 1.24253266
+6 1.03785456 1.85913227 0.41941927
+7 1.89591794 2.52502498 0.45781397
+8 0.56446512 2.04885953 -0.54109826
+9 1.52620322 0.40323380 0.43165058
+10 1.74209070 0.08202393 1.44927248
+11 2.47052411 0.35460290 -0.10442391
+12 0.55827298 -0.57733956 -0.24329508
+13 1.06596662 -1.52840251 -0.38743543
+14 0.33513856 -0.20190168 -1.24074560
+15 -0.75555527 -0.85112842 0.49451822
+16 -0.54370295 -1.41365165 1.40244792
+17 -1.36009398 -1.50546676 -0.12952032
+18 -1.59017203 0.37813982 0.87698035
+19 -2.55880030 0.02409637 1.22033854
+20 -1.78852917 0.98939742 -0.00185751
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 9 11
+9 10 6 9 12 14 12 13
+9 12 15 17 15 16 12 15
+0 3 0 18 15 18 18 19
+18 20
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 11 9 10 8 6 9
+7 6 9 3 6 9 6 9 11
+6 9 10 14 12 13 11 9 12
+10 9 12 6 9 12 9 12 14
+9 12 13 17 15 16 14 12 15
+13 12 15 9 12 15 12 15 17
+12 15 16 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+1 0 18 2 0 18 3 0 18
+17 15 18 16 15 18 12 15 18
+15 18 0 0 18 19 15 18 19
+0 18 20 15 18 20 19 18 20
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+8 6 9 11 8 6 9 10
+7 6 9 11 7 6 9 10
+3 6 9 11 3 6 9 10
+11 9 12 14 11 9 12 13
+10 9 12 14 10 9 12 13
+6 9 12 14 6 9 12 13
+14 12 15 17 14 12 15 16
+13 12 15 17 13 12 15 16
+9 12 15 17 9 12 15 16
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+15 0 3 5 15 0 3 4
+15 0 3 6 5 3 6 9
+4 3 6 9 0 3 6 8
+0 3 6 7 0 3 6 9
+8 6 9 12 7 6 9 12
+3 6 9 12 11 9 12 15
+10 9 12 15 6 9 12 15
+14 12 15 0 13 12 15 0
+9 12 15 0 17 15 18 0
+16 15 18 0 12 15 18 0
+18 0 3 5 18 0 3 4
+18 0 3 6 1 0 18 15
+1 0 18 19 1 0 18 20
+2 0 18 15 2 0 18 19
+2 0 18 20 3 0 18 15
+3 0 18 19 3 0 18 20
+14 12 15 18 13 12 15 18
+9 12 15 18 17 15 18 19
+17 15 18 20 16 15 18 19
+16 15 18 20 12 15 18 19
+12 15 18 20
+
+!:md_parameters
+log_file cyclohexane.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 23172
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 -0.00000027 -0.00000005 0.00000017
+1 0.00000006 0.00000003 0.00000003
+2 0.00000018 -0.00000015 -0.00000003
+3 -0.00000008 -0.00000010 -0.00000015
+4 0.00000009 0.00000016 0.00000013
+5 -0.00000009 0.00000000 -0.00000006
+6 0.00000016 0.00000017 -0.00000010
+7 -0.00000019 -0.00000008 -0.00000004
+8 0.00000004 -0.00000002 0.00000004
+9 0.00000009 -0.00000029 -0.00000005
+10 0.00000001 0.00000001 0.00000005
+11 -0.00000026 0.00000007 0.00000012
+12 0.00000029 0.00000004 -0.00000015
+13 -0.00000005 -0.00000004 -0.00000008
+14 -0.00000003 -0.00000001 0.00000009
+15 -0.00000014 0.00000016 0.00000007
+16 0.00000001 -0.00000002 0.00000000
+17 0.00000002 -0.00000000 0.00000000
+18 -0.00000013 -0.00000002 0.00000010
+19 0.00000022 0.00000014 -0.00000019
+20 0.00000005 0.00000000 0.00000005
+
+!:force
+! idx fx fy fz
+0 -0.00000027 -0.00000005 0.00000017
+1 0.00000006 0.00000003 0.00000003
+2 0.00000018 -0.00000015 -0.00000003
+3 -0.00000008 -0.00000010 -0.00000015
+4 0.00000009 0.00000016 0.00000013
+5 -0.00000009 0.00000000 -0.00000006
+6 0.00000016 0.00000017 -0.00000010
+7 -0.00000019 -0.00000008 -0.00000004
+8 0.00000004 -0.00000002 0.00000004
+9 0.00000009 -0.00000029 -0.00000005
+10 0.00000001 0.00000001 0.00000005
+11 -0.00000026 0.00000007 0.00000012
+12 0.00000029 0.00000004 -0.00000015
+13 -0.00000005 -0.00000004 -0.00000008
+14 -0.00000003 -0.00000001 0.00000009
+15 -0.00000014 0.00000016 0.00000007
+16 0.00000001 -0.00000002 0.00000000
+17 0.00000002 -0.00000000 0.00000000
+18 -0.00000013 -0.00000002 0.00000010
+19 0.00000022 0.00000014 -0.00000019
+20 0.00000005 0.00000000 0.00000005
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+256.449005 0.879324 0.210719 0.427068
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CHX C1 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CHX H11 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CHX H12 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CHX C2 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CHX H21 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CHX H22 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CHX C3 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CHX H31 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CHX H32 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 CHX C4 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 CHX H41 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 CHX H42 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 CHX C5 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 CHX H51 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 CHX H52 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+15 MAIN 1 CHX C6 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+16 MAIN 1 CHX H61 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+17 MAIN 1 CHX H62 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.37191979 -0.01470847 -0.04533071
+1 -0.75956029 -0.01758412 -1.06061947
+2 -0.69639261 -0.94754613 0.41364630
+3 1.15921830 0.03103315 -0.06545907
+4 1.55271053 -0.83785433 -0.58630743
+5 1.48408579 0.90448274 -0.62908631
+6 1.73647111 0.10263286 1.35176821
+7 2.81961168 0.18159574 1.31107702
+8 1.51218359 -0.82462353 1.87714401
+9 1.15083751 1.28073591 2.13661683
+10 1.53848192 1.28362024 3.15190405
+11 1.47530662 2.21357078 1.67763142
+12 -0.38030014 1.23499061 2.15674936
+13 -0.77379399 2.10387643 2.67759924
+14 -0.70516396 0.36153957 2.72037649
+15 -0.95755584 1.16339033 0.73952318
+16 -2.04069583 1.08442098 0.78021752
+17 -0.73327535 2.09064904 0.21414856
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 4 3 5
+6 8 6 7 3 6 9 10
+9 11 6 9 12 14 12 13
+9 12 15 16 15 17 12 15
+0 3 0 15
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 4 3 5 8 6 7
+4 3 6 5 3 6 3 6 8
+3 6 7 10 9 11 8 6 9
+7 6 9 3 6 9 6 9 10
+6 9 11 14 12 13 10 9 12
+11 9 12 6 9 12 9 12 14
+9 12 13 16 15 17 14 12 15
+13 12 15 9 12 15 12 15 16
+12 15 17 1 0 3 2 0 3
+0 3 4 0 3 5 0 3 6
+1 0 15 2 0 15 3 0 15
+0 15 16 0 15 17 0 15 12
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+4 3 6 8 4 3 6 7
+5 3 6 8 5 3 6 7
+8 6 9 10 8 6 9 11
+7 6 9 10 7 6 9 11
+3 6 9 10 3 6 9 11
+10 9 12 14 10 9 12 13
+11 9 12 14 11 9 12 13
+6 9 12 14 6 9 12 13
+14 12 15 16 14 12 15 17
+13 12 15 16 13 12 15 17
+9 12 15 16 9 12 15 17
+1 0 3 4 1 0 3 5
+1 0 3 6 2 0 3 4
+2 0 3 5 2 0 3 6
+1 0 15 16 1 0 15 17
+1 0 15 12 2 0 15 16
+2 0 15 17 2 0 15 12
+3 0 15 16 3 0 15 17
+3 0 15 12 15 0 3 4
+15 0 3 5 15 0 3 6
+4 3 6 9 5 3 6 9
+0 3 6 8 0 3 6 7
+0 3 6 9 8 6 9 12
+7 6 9 12 3 6 9 12
+10 9 12 15 11 9 12 15
+6 9 12 15 14 12 15 0
+13 12 15 0 9 12 15 0
+
+!:md_parameters
+log_file (null)
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 96
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+15 0.00000000 0.00000000 0.00000000
+16 0.00000000 0.00000000 0.00000000
+17 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+15 0.00000000 0.00000000 0.00000000
+16 0.00000000 0.00000000 0.00000000
+17 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+217.841995 0.991193 -0.132331 0.004939
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 COC C1 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 COC H11 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 COC H12 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 COC C2 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 COC H21 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 COC H22 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 COC C3 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 COC H31 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 COC H32 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 COC C4 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 COC H41 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 COC H42 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 COC C5 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 COC H51 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 COC H52 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+15 MAIN 1 COC C6 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+16 MAIN 1 COC H61 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+17 MAIN 1 COC H62 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+18 MAIN 1 COC C7 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+19 MAIN 1 COC H71 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+20 MAIN 1 COC H72 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+21 MAIN 1 COC C8 c3 0.01240 12.01070 C 6 1.000000 0.000000 0
+22 MAIN 1 COC H81 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+23 MAIN 1 COC H82 hc -0.00620 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.66312953 2.55560040 1.44151503
+1 -0.24003870 2.93020471 2.37176320
+2 -1.26639227 3.36782871 1.04073779
+3 0.48550936 2.28894637 0.45334412
+4 1.30877418 1.79393637 0.95729663
+5 0.87489894 3.25903959 0.15636121
+6 0.11133543 1.49585495 -0.81567033
+7 0.65250615 1.92174377 -1.65639178
+8 -0.94187946 1.63512556 -1.04839059
+9 0.45099422 -0.00259668 -0.79681401
+10 1.52348903 -0.10483043 -0.63666494
+11 0.26199665 -0.39350892 -1.79438113
+12 -0.27099554 -0.91910061 0.20310244
+13 0.04217528 -1.93329755 -0.03010992
+14 -1.34281999 -0.89736196 0.01997282
+15 0.01975153 -0.65298693 1.69442612
+16 0.99495451 -0.18830768 1.79352375
+17 0.10461013 -1.60641354 2.20889743
+18 -1.04148738 0.16571678 2.44971057
+19 -0.63133495 0.45860458 3.41443209
+20 -1.87788886 -0.49465872 2.67016519
+21 -1.62005924 1.40020579 1.75123433
+22 -2.40599776 1.79473869 2.39150882
+23 -2.12232450 1.09468064 0.83850906
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 9 11
+9 10 6 9 12 14 12 13
+9 12 15 17 15 16 12 15
+0 3 15 18 18 19 18 20
+18 21 21 0 21 23 21 22
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 11 9 10 8 6 9
+7 6 9 3 6 9 6 9 11
+6 9 10 14 12 13 11 9 12
+10 9 12 6 9 12 9 12 14
+9 12 13 17 15 16 14 12 15
+13 12 15 9 12 15 12 15 17
+12 15 16 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+17 15 18 16 15 18 12 15 18
+15 18 19 15 18 20 19 18 20
+15 18 21 19 18 21 20 18 21
+18 21 0 21 0 1 21 0 2
+21 0 3 18 21 23 0 21 23
+18 21 22 0 21 22 23 21 22
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+8 6 9 11 8 6 9 10
+7 6 9 11 7 6 9 10
+3 6 9 11 3 6 9 10
+11 9 12 14 11 9 12 13
+10 9 12 14 10 9 12 13
+6 9 12 14 6 9 12 13
+14 12 15 17 14 12 15 16
+13 12 15 17 13 12 15 16
+9 12 15 17 9 12 15 16
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+15 0 3 5 15 0 3 4
+15 0 3 6 5 3 6 9
+4 3 6 9 0 3 6 8
+0 3 6 7 0 3 6 9
+8 6 9 12 7 6 9 12
+3 6 9 12 11 9 12 15
+10 9 12 15 6 9 12 15
+14 12 15 0 13 12 15 0
+9 12 15 0 17 15 18 0
+16 15 18 0 12 15 18 0
+18 0 3 5 18 0 3 4
+18 0 3 6 14 12 15 18
+13 12 15 18 9 12 15 18
+17 15 18 19 17 15 18 20
+16 15 18 19 16 15 18 20
+12 15 18 19 12 15 18 20
+18 21 0 1 18 21 0 2
+18 21 0 3 21 0 3 5
+21 0 3 4 21 0 3 6
+1 0 21 23 1 0 21 22
+2 0 21 23 2 0 21 22
+3 0 21 23 3 0 21 22
+17 15 18 21 16 15 18 21
+12 15 18 21 15 18 21 0
+15 18 21 23 15 18 21 22
+19 18 21 0 19 18 21 23
+19 18 21 22 20 18 21 0
+20 18 21 23 20 18 21 22
+
+!:md_parameters
+log_file cyclohexane.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 34552
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 -0.00000001 -0.00000004 -0.00000027
+1 0.00000011 0.00000020 0.00000014
+2 -0.00000001 -0.00000005 0.00000014
+3 0.00000030 -0.00000008 0.00000008
+4 0.00000016 0.00000005 0.00000011
+5 -0.00000020 0.00000008 0.00000001
+6 0.00000020 0.00000024 -0.00000046
+7 -0.00000033 0.00000000 -0.00000002
+8 -0.00000011 -0.00000019 -0.00000008
+9 -0.00000008 -0.00000024 0.00000024
+10 0.00000005 0.00000010 -0.00000015
+11 0.00000004 0.00000006 0.00000010
+12 0.00000012 0.00000004 -0.00000021
+13 0.00000001 -0.00000006 0.00000021
+14 -0.00000010 -0.00000009 -0.00000013
+15 -0.00000034 0.00000015 0.00000022
+16 0.00000024 0.00000002 0.00000024
+17 0.00000018 -0.00000003 0.00000006
+18 0.00000017 0.00000001 -0.00000003
+19 -0.00000009 -0.00000001 -0.00000020
+20 -0.00000027 -0.00000011 -0.00000032
+21 -0.00000039 -0.00000026 0.00000035
+22 0.00000021 0.00000007 0.00000001
+23 0.00000013 0.00000013 -0.00000004
+
+!:force
+! idx fx fy fz
+0 -0.00000001 -0.00000004 -0.00000027
+1 0.00000011 0.00000020 0.00000014
+2 -0.00000001 -0.00000005 0.00000014
+3 0.00000030 -0.00000008 0.00000008
+4 0.00000016 0.00000005 0.00000011
+5 -0.00000020 0.00000008 0.00000001
+6 0.00000020 0.00000024 -0.00000046
+7 -0.00000033 0.00000000 -0.00000002
+8 -0.00000011 -0.00000019 -0.00000008
+9 -0.00000008 -0.00000024 0.00000024
+10 0.00000005 0.00000010 -0.00000015
+11 0.00000004 0.00000006 0.00000010
+12 0.00000012 0.00000004 -0.00000021
+13 0.00000001 -0.00000006 0.00000021
+14 -0.00000010 -0.00000009 -0.00000013
+15 -0.00000034 0.00000015 0.00000022
+16 0.00000024 0.00000002 0.00000024
+17 0.00000018 -0.00000003 0.00000006
+18 0.00000017 0.00000001 -0.00000003
+19 -0.00000009 -0.00000001 -0.00000020
+20 -0.00000027 -0.00000011 -0.00000032
+21 -0.00000039 -0.00000026 0.00000035
+22 0.00000021 0.00000007 0.00000001
+23 0.00000013 0.00000013 -0.00000004
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+178.717422 0.567078 0.725464 0.390031
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CPN C1 c3 0.01523 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CPN H11 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CPN H12 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CPN C2 c3 0.01523 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CPN H21 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CPN H22 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CPN C3 c3 0.01523 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CPN H31 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CPN H32 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 CPN C4 c3 0.01523 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 CPN H41 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 CPN H42 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 CPN C5 c3 0.01523 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 CPN H51 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 CPN H52 hc -0.00762 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.19744991 0.23585164 0.43220845
+1 -0.21422703 1.04106825 -0.29904357
+2 -1.03249136 -0.42078992 0.21081692
+3 1.15684933 -0.48657856 0.39489067
+4 1.53667092 -0.61145021 -0.61339689
+5 1.04704831 -1.48170012 0.81644562
+6 2.09814572 0.36536213 1.28331184
+7 2.82528872 0.90360556 0.68489399
+8 2.66205483 -0.26464352 1.96276076
+9 1.18315997 1.34912793 2.05534299
+10 1.26684228 2.34578038 1.63140389
+11 1.44925240 1.42909785 3.10381976
+12 -0.24390233 0.82321468 1.84499292
+13 -0.99962524 1.59223952 1.96735132
+14 -0.46335659 0.03470786 2.56157300
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 9 11
+9 10 6 9 12 14 12 13
+9 12 0 3 0 12
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 11 9 10 8 6 9
+7 6 9 3 6 9 6 9 11
+6 9 10 14 12 13 11 9 12
+10 9 12 6 9 12 9 12 14
+9 12 13 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+1 0 12 2 0 12 3 0 12
+0 12 14 0 12 13 0 12 9
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+8 6 9 11 8 6 9 10
+7 6 9 11 7 6 9 10
+3 6 9 11 3 6 9 10
+11 9 12 14 11 9 12 13
+10 9 12 14 10 9 12 13
+6 9 12 14 6 9 12 13
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+5 3 6 9 4 3 6 9
+0 3 6 8 0 3 6 7
+0 3 6 9 8 6 9 12
+7 6 9 12 3 6 9 12
+1 0 12 14 1 0 12 13
+1 0 12 9 2 0 12 14
+2 0 12 13 2 0 12 9
+3 0 12 14 3 0 12 13
+3 0 12 9 12 0 3 5
+12 0 3 4 12 0 3 6
+11 9 12 0 10 9 12 0
+6 9 12 0
+
+!:md_parameters
+log_file cyclopentane.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 123
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+126.035088 -0.950792 0.110747 -0.289361
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CPP C1 c3 -0.25091 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CPP H11 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CPP H12 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CPP C2 c3 -0.25091 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CPP H21 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CPP H22 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CPP C3 c3 -0.25091 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CPP H31 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CPP H32 hc 0.12546 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 0.43402633 0.34672893 0.72715097
+1 0.14003774 1.18801304 0.12444481
+2 -0.31830214 0.02387227 1.42515412
+3 1.31409933 -0.69352818 0.10623366
+4 1.61644299 -0.55711709 -0.91720332
+5 1.15810297 -1.72125782 0.38350580
+6 1.87020247 0.23933899 1.13711198
+7 2.54935753 1.00785618 0.81219247
+8 2.09101732 -0.15628438 2.11290186
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 0 3
+0 6
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+1 0 6 2 0 6 3 0 6
+0 6 8 0 6 7 0 6 3
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+0 3 6 8 0 3 6 7
+1 0 6 8 1 0 6 7
+1 0 6 3 2 0 6 8
+2 0 6 7 2 0 6 3
+3 0 6 8 3 0 6 7
+6 0 3 5 6 0 3 4
+5 3 6 0 4 3 6 0
+
+!:md_parameters
+log_file cyclopentane.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 141
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3 2815 0.0040 0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664 0.0043 0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380 0.7199 0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092 0.5379 0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3 507 1.7605 2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+44.344196 -0.681719 0.674688 -0.282940
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 RES C1 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 RES H1 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 RES C2 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 RES H2 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 RES C3 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 RES H3 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 RES C4 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 RES H4 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 RES C5 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 RES H5 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+10 MAIN 1 RES C6 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+11 MAIN 1 RES H6 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.65300000 0.58500000 -1.06800000
+1 -1.15800000 1.03900000 -1.89800000
+2 0.72900000 0.60700000 -1.00300000
+3 1.29500000 1.07600000 -1.78300000
+4 1.38200000 0.02100000 0.06900000
+5 2.45200000 0.03800000 0.11900000
+6 0.65100000 -0.58600000 1.07600000
+7 1.15600000 -1.03900000 1.90600000
+8 -0.73200000 -0.60700000 1.01200000
+9 -1.29800000 -1.07700000 1.79200000
+10 -1.38400000 -0.02100000 -0.06000000
+11 -2.45500000 -0.03800000 -0.11000000
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 10 2 3
+2 4 4 5 4 6 6 7
+6 8 8 9 8 10 10 11
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 10 0 1 10 0 2
+0 2 3 0 2 4 0 10 8
+0 10 11 4 2 3 2 4 5
+2 4 6 6 4 5 4 6 7
+4 6 8 8 6 7 6 8 9
+6 8 10 10 8 9 8 10 11
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 1 0 2 4
+10 0 2 3 10 0 2 4
+1 0 10 8 1 0 10 11
+2 0 10 8 2 0 10 11
+0 2 4 5 0 2 4 6
+3 2 4 5 3 2 4 6
+2 4 6 7 2 4 6 8
+5 4 6 7 5 4 6 8
+4 6 8 9 4 6 8 10
+7 6 8 9 7 6 8 10
+6 8 10 0 6 8 10 11
+9 8 10 0 9 8 10 11
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+0.000000 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CHT C1 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CHT H1 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CHT C2 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 CHT H2 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 CHT C3 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 CHT H3 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CHT C4 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CHT H4 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CHT C5 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 CHT H5 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+10 MAIN 1 CHT C6 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+11 MAIN 1 CHT H6 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 CHT C7 ca -0.02129 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 CHT H7 ha 0.16415 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.45073110 0.53625132 -0.89823177
+1 -0.94225597 1.05190512 -1.70321941
+2 0.93614286 0.60682562 -0.89526880
+3 1.37621020 1.16988561 -1.69826623
+4 1.82968755 0.04619185 0.00787934
+5 2.86996750 0.23266276 -0.18845438
+6 1.55704565 -0.72348142 1.13112386
+7 2.41418620 -1.05401597 1.68929739
+8 0.32352194 -1.12261510 1.62863819
+9 0.35207878 -1.72125766 2.52100149
+10 -0.94201496 -0.85065125 1.12578535
+11 -1.76354574 -1.26660838 1.68037308
+12 -1.28659002 -0.11238709 0.00122191
+13 -2.33957904 -0.03243770 -0.19958384
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 12 2 3
+2 4 4 5 8 9 8 10
+10 11 10 12 12 13 6 7
+4 6 6 8
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 12 0 1 12 0 2
+0 2 3 0 2 4 0 12 10
+0 12 13 4 2 3 2 4 5
+10 8 9 8 10 11 8 10 12
+12 10 11 10 12 13 2 4 6
+5 4 6 4 6 7 7 6 8
+4 6 8 6 8 9 6 8 10
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 1 0 2 4
+12 0 2 3 12 0 2 4
+1 0 12 10 1 0 12 13
+2 0 12 10 2 0 12 13
+0 2 4 5 0 2 4 8
+3 2 4 5 3 2 4 8
+4 8 10 11 4 8 10 12
+9 8 10 11 9 8 10 12
+8 10 12 0 8 10 12 13
+11 10 12 0 11 10 12 13
+2 4 6 7 5 4 6 7
+7 6 8 9 7 6 8 10
+4 6 8 9 4 6 8 10
+0 2 4 6 3 2 4 6
+2 4 6 8 5 4 6 8
+6 8 10 11 6 8 10 12
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 2 0 12 0 3 2 4
+2 5 4 6 9 10 8 6
+8 11 10 12 0 10 12 13
+7 4 6 8
+
+!:md_parameters
+log_file (null)
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 8
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+! type1 type2 type3 k a0
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+! type1 type2 type3 type4 k periodicity phi0
+impr ha X ca X 1.100000 2 180.000005 ![gaff] bsd.on C6H6 nmodes
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+46.053040 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CPD C1 ca -0.29343 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CPD H1 ha 0.09343 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CPD C2 ca -0.29343 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 CPD H2 ha 0.09343 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 CPD C3 ca -0.29343 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 CPD H3 ha 0.09343 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CPD C4 ca -0.29343 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CPD H4 ha 0.09343 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CPD C5 ca -0.29343 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 CPD H5 ha 0.09343 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.74399479 0.66664983 -1.21653356
+1 -1.25264934 1.12329268 -2.05270999
+2 0.64411134 0.61523112 -1.02440933
+3 1.39226171 1.02531874 -1.68663465
+4 0.89028323 -0.06212266 0.17849780
+5 1.86132012 -0.26531740 0.60539654
+6 -0.34568018 -0.42933165 0.72981105
+7 -0.49369660 -0.96500155 1.65587377
+8 -1.35571960 0.02107432 -0.13236595
+9 -2.41823578 -0.10679205 0.01307413
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 8 2 3
+2 4 4 5 6 7 6 8
+8 9 6 4
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 8 0 1 8 0 2
+0 2 3 0 2 4 0 8 6
+0 8 9 4 2 3 2 4 5
+8 6 7 6 8 9 7 6 4
+8 6 4 6 4 2 6 4 5
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 1 0 2 4
+8 0 2 3 8 0 2 4
+1 0 8 6 1 0 8 9
+2 0 8 6 2 0 8 9
+0 2 4 5 3 2 4 5
+7 6 8 0 7 6 8 9
+7 6 4 2 7 6 4 5
+8 6 4 2 8 6 4 5
+0 2 4 6 3 2 4 6
+4 6 8 0 4 6 8 9
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 2 0 8 0 3 2 4
+2 5 4 6 7 8 6 4
+0 6 8 9
+
+!:md_parameters
+log_file (null)
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 5
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+! type1 type2 type3 k a0
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+! type1 type2 type3 type4 k periodicity phi0
+impr ha X ca X 1.100000 2 180.000005 ![gaff] bsd.on C6H6 nmodes
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+#
+# This script is loaded from formula.rb
+#
+
+class Molecule
+
+ # "fragment name", "mbsf name" | "other fragment name", "dummy atoms"
+ table = [
+ "Alicyclic",
+ ["cyclopropane", "alicyclic/cyclopropane.mbsf"],
+ ["C3H6", "cyclopropane"],
+ ["cyclopropyl", "cyclopropane", "H11"],
+ ["C3H5", "cyclopropyl"],
+
+ ["cyclobutane", "alicyclic/cyclobutane.mbsf"],
+ ["C4H8", "cyclobutane"],
+ ["cyclobutyl", "cyclobutane", "H11"],
+ ["C4H7", "cyclobutyl"],
+
+ ["cyclopentane", "alicyclic/cyclopentane.mbsf"],
+ ["C5H10", "cyclopentane"],
+ ["cyclopentyl", "cyclopentane", "H11"],
+ ["C5H9", "cyclopentyl"],
+
+ ["cyclohexane", "alicyclic/cyclohexane.mbsf"],
+ ["C6H12", "cyclohexane"],
+ ["cyclohexyl", "cyclohexane", "H11"],
+ ["C6H11", "cyclohexyl"],
+ ["Cy", "cyclohexyl"],
+
+ ["cycloheptane", "alicyclic/cycloheptane.mbsf"],
+ ["C7H14", "cycloheptane"],
+ ["cycloheptyl", "cycloheptane", "H11"],
+ ["C7H13", "cycloheptyl"],
+
+ ["cyclooctane", "alicyclic/cyclooctane.mbsf"],
+ ["C8H16", "cyclooctane"],
+ ["cyclooctyl", "cyclooctane", "H11"],
+ ["C8H15", "cyclooctyl"],
+
+ "Aromatic",
+ ["benzene", "aromatic/benzene.mbsf"],
+ ["C6H6", "benzene"],
+ ["C6H5", "benzene", "H1"],
+ ["Ph", "C6H5"],
+ ["phenyl", "C6H5"],
+ ["C6H4", "benzene", "H1", "H4"],
+ ["C6H3", "benzene", "H1", "H3", "H5"],
+
+ ["cyclopentadienyl", "aromatic/cyclopentadienyl.mbsf"],
+ ["C5H5", "cyclopentadienyl"],
+ ["Cp", "cyclopentadienyl"],
+ ["C5H4", "cyclopentadienyl", "H1"],
+
+ ["cycloheptatrienyl", "aromatic/cycloheptatrienyl.mbsf"],
+ ["C7H7", "cycloheptatrienyl"],
+ ["C7H6", "cycloheptatrienyl", "H1"],
+
+ "Heterocyclic",
+ ["furan", "heterocyclic/furan.mbsf"],
+ ["imidazole", "heterocyclic/imidazole.mbsf"],
+ ["oxazole", "heterocyclic/oxazole.mbsf"],
+ ["phthalocyanine", "heterocyclic/phthalocyanine.mbsf"],
+ ["porphine", "heterocyclic/porphine.mbsf"],
+ ["pyrazine", "heterocyclic/pyrazine.mbsf"],
+ ["pyrazole", "heterocyclic/pyrazole.mbsf"],
+ ["pyridazine", "heterocyclic/pyridazine.mbsf"],
+ ["pyridine", "heterocyclic/pyridine.mbsf"],
+ ["pyrimidine", "heterocyclic/pyrimidine.mbsf"],
+ ["pyrrole", "heterocyclic/pyrrole.mbsf"],
+ ["thiazole", "heterocyclic/thiazole.mbsf"],
+ ["thiophene", "heterocyclic/thiophene.mbsf"]
+ ]
+
+ $named_fragments = []
+
+ table.each { |t|
+ if t.is_a?(String)
+ $named_fragments.push([t, "-"]) # Subtitle
+ next
+ end
+ fname = t[1]
+ if fname =~ /\.mbsf$/
+ f = new(MbsfPath + "/" + fname) # Molecule.new
+ $named_fragments.push([t[0], t[1]]) # Registered fragment
+ else
+ f = known_fragment(fname)
+ end
+ (2...t.length).each { |i|
+ p = f.atoms[t[i]]
+ if p
+ p.name = "_#{i - 1}"
+ p.atom_type = ""
+ p.element = "Du"
+ end
+ }
+ f.dummies = f.find_dummy_atoms
+ register_fragment(t[0], f)
+ }
+
+ $named_fragments.concat([ # Non-registered fragments
+ ["Solvent boxes", "-"],
+ ["CHCl3", "solvents/chcl3box.mbsf"],
+ ["DMSO", "solvents/dmsobox.mbsf"],
+ ["MeOH", "solvents/meohbox.mbsf"],
+ ["N-methylacetamide", "solvents/nmabox.mbsf"],
+ ["H2O (tip3p)", "solvents/tip3pbox.mbsf"]])
+
+end
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 FUR O1 os -0.17286 15.99940 O 8 1.000000 0.000000 0
+1 MAIN 1 FUR C2 cc -0.04429 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 FUR H2 h4 0.16699 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 FUR C3 cd -0.19754 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 FUR H3 ha 0.16127 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 FUR C4 cd -0.19754 12.01070 C 6 1.000000 0.000000 0
+6 MAIN 1 FUR H4 ha 0.16127 1.00790 H 1 1.000000 0.000000 0
+7 MAIN 1 FUR C5 cc -0.04429 12.01070 C 6 1.000000 0.000000 0
+8 MAIN 1 FUR H5 h4 0.16699 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.70821283 0.64099817 -1.16903126
+1 0.61918917 0.58211335 -0.96831686
+2 1.22893560 1.03653969 -1.71828494
+3 0.89968848 -0.05884065 0.17344882
+4 1.87152732 -0.24973884 0.57889776
+5 -0.37499552 -0.43198627 0.73229588
+6 -0.55848259 -0.96108936 1.64426304
+7 -1.29357558 0.02217875 -0.12972247
+8 -2.36090713 -0.01433548 -0.14442606
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 7 1 2 1 3
+5 6 5 7 7 8 5 3
+3 4
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+7 0 1 0 1 2 0 1 3
+0 7 5 0 7 8 3 1 2
+7 5 6 5 7 8 6 5 3
+7 5 3 5 3 1 1 3 4
+5 3 4
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+7 0 1 2 7 0 1 3
+1 0 7 5 1 0 7 8
+6 5 7 0 6 5 7 8
+6 5 3 1 7 5 3 1
+0 1 3 5 2 1 3 5
+3 5 7 0 3 5 7 8
+0 1 3 4 2 1 3 4
+4 3 5 6 4 3 5 7
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+0 2 1 3 6 7 5 3
+0 5 7 8 1 5 3 4
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 18
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond cc os 376.100002 1.370000 ![gaff] SOURCE3 86 0.0139 0.0192
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cd ha 347.200012 1.085000 ![gaff] SOURCE3 740 0.0029 0.0039
+bond cd cd 418.299991 1.429000 ![gaff] SOURCE1 740 0.0058 0.0069
+! type1 type2 type3 k a0
+angle cc os cc 66.500002 109.170001 ![gaff] SOURCE3 12 6.7381 7.2529
+angle h4 cc os 52.300000 111.890001 ![gaff] SOURCE3 61 1.5084 2.3500
+angle cd cc os 69.999999 120.299999 ![gaff] SOURCE3 64 3.4271 5.4354
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cc cd ha 48.400002 122.889993 ![gaff] SOURCE3 584 2.3225 2.9334
+angle cd cd ha 46.599998 123.739996 ![gaff] SOURCE3 656 2.7165 3.3195
+angle cc cd cd 68.199995 114.190005 ![gaff] SOURCE3 517 5.4334 6.5960
+angle na c2 os 73.885003 112.565001 ! Calculated with empirical approach
+angle h5 c2 os 51.700000 116.110006 ! same as hc-c2-os
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe X cd cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe cc os cc h4 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cc os cc cd 1.050000 2 180.000005 ! same as X -c2-os-X
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na cc nd 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd nd 1.100000 2 180.000005 ! Using default value
+impr h5 na c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 na 1.100000 2 180.000005 ! Using default value
+impr c2 c2 na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr cd h4 cc os 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw os 0.170000 1.683700 0.170000 1.683700 8 16.000000 ![gaff] Ether and ester oxygen
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 IMD N1 na -0.19265 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 IMD H1 hn 0.29916 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 IMD C2 cc 0.15209 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 IMD H2 h5 0.12672 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 IMD N3 nd -0.50225 14.00670 N 7 1.000000 0.000000 0
+5 MAIN 1 IMD C4 cd 0.09749 12.01070 C 6 1.000000 0.000000 0
+6 MAIN 1 IMD H4 h4 0.11938 1.00790 H 1 1.000000 0.000000 0
+7 MAIN 1 IMD C5 cc -0.30142 12.01070 C 6 1.000000 0.000000 0
+8 MAIN 1 IMD H5 h4 0.20147 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.72974376 0.64744237 -1.18188717
+1 -1.16861793 1.07566723 -1.96322064
+2 0.59725992 0.57067037 -0.94991552
+3 1.31908575 0.98594477 -1.62315044
+4 0.86468174 -0.04668130 0.14960326
+5 -0.35324068 -0.39754830 0.67366030
+6 -0.42922385 -0.92961031 1.59871681
+7 -1.35253941 0.02111303 -0.13219871
+8 -2.41550936 -0.06242773 -0.06432532
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 7 2 3
+2 4 5 6 5 7 7 8
+5 4
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 7 0 1 7 0 2
+0 2 3 0 2 4 0 7 5
+0 7 8 4 2 3 7 5 6
+5 7 8 6 5 4 7 5 4
+5 4 2
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 1 0 2 4
+7 0 2 3 7 0 2 4
+1 0 7 5 1 0 7 8
+2 0 7 5 2 0 7 8
+6 5 7 0 6 5 7 8
+6 5 4 2 7 5 4 2
+0 2 4 5 3 2 4 5
+4 5 7 0 4 5 7 8
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 2 0 7 0 3 2 4
+6 7 5 4 0 5 7 8
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 12
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond hn na 406.600015 1.011000 ![gaff] SOURCE3 46 0.0076 0.0107
+bond cc na 438.799985 1.371000 ![gaff] SOURCE3 440 0.0107 0.0144
+bond cc h5 355.999995 1.079000 ![gaff] SOURCE3 40 0.0040 0.0051
+bond cc nd 494.599991 1.335000 ![gaff] SOURCE3 203 0.0171 0.0239
+bond cd h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cd nd 431.599989 1.376000 ![gaff] SOURCE1 88 0.0000 0.0000
+! type1 type2 type3 k a0
+angle cc na hn 47.200002 124.660009 ![gaff] SOURCE3 38 4.3279 5.9689
+angle cc na cc 68.900001 109.900005 ![gaff] SOURCE3 109 1.2152 1.5547
+angle h5 cc na 49.799999 122.100000 ![gaff] SOURCE3 16 1.2773 1.4626
+angle na cc nd 74.800001 112.020000 ![gaff] SOURCE3 17 1.9564 2.2434
+angle cd cc na 72.900000 109.419999 ![gaff] SOURCE3 265 1.3410 2.6051
+angle h4 cc na 50.200001 119.660010 ![gaff] SOURCE3 294 0.9445 2.4702
+angle h5 cc nd 50.099999 125.379993 ![gaff] SOURCE3 40 1.6952 2.2157
+angle cc cd h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle h4 cd nd 49.999998 120.030002 ![gaff] SOURCE3 16 1.9828 2.3863
+angle cc cd nd 71.000000 114.980006 ![gaff] SOURCE3 23 4.6219 5.3935
+angle cc nd cd 70.500001 107.470001 ![gaff] SOURCE3 26 4.9214 5.4053
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cc na X 1.700000 2 180.000005 ![gaff] statistic value from parm94
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe X cd nd X 4.750000 2 180.000005 ![gaff] statistiv value from parm94
+dihe X cc nd X 4.750000 2 180.000005 ![gaff] statistic value from parm94
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na cc nd 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd nd 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw na 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N with three connected atoms
+vdw hn 0.015700 0.600000 0.015700 0.600000 1 1.008000 ![gaff] H bonded to nitrogen atoms
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+vdw h5 0.015000 1.359000 0.015000 1.359000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 2 electrwd. group
+vdw nd 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in non-pure aromatic systems, identical to nc
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 OXZ N1 nc -0.53721 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 OXZ C2 cd 0.41800 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 OXZ H2 h5 0.08736 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 OXZ O3 os -0.24385 15.99940 O 8 1.000000 0.000000 0
+4 MAIN 1 OXZ C4 cd -0.09815 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 OXZ H4 h4 0.17719 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 OXZ C5 cc 0.05739 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 OXZ H5 h4 0.13928 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.70644780 0.66810207 -1.21630979
+1 0.53426129 0.57810646 -0.96755982
+2 1.34974126 0.94658124 -1.55204147
+3 0.83606355 -0.05461842 0.16138065
+4 -0.36223053 -0.40573314 0.68731595
+5 -0.35320382 -0.93465971 1.61314650
+6 -1.31082147 0.02872230 -0.14243747
+7 -2.37263499 -0.06111042 -0.06347354
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 6 1 2 1 3
+4 5 4 6 6 7 4 3
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+6 0 1 0 1 2 0 1 3
+0 6 4 0 6 7 3 1 2
+6 4 5 4 6 7 5 4 3
+6 4 3 4 3 1
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+6 0 1 2 6 0 1 3
+1 0 6 4 1 0 6 7
+5 4 6 0 5 4 6 7
+5 4 3 1 6 4 3 1
+0 1 3 4 2 1 3 4
+3 4 6 0 3 4 6 7
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+0 2 1 3 5 6 4 3
+0 4 6 7
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 18
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond cd nc 494.599991 1.335000 ![gaff] SOURCE3 203 0.0171 0.0239
+bond cc nc 431.599989 1.376000 ![gaff] SOURCE1 88 0.0000 0.0000
+bond cd h5 355.999995 1.079000 ![gaff] SOURCE3 40 0.0040 0.0051
+bond cd os 376.100002 1.370000 ![gaff] SOURCE3 86 0.0139 0.0192
+bond cd h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+! type1 type2 type3 k a0
+angle cc nc cd 70.500001 107.470001 ![gaff] SOURCE3 26 4.9214 5.4053
+angle h5 cd nc 50.099999 125.379993 ![gaff] SOURCE3 40 1.6952 2.2157
+angle nc cd os 73.000002 119.140001 ![gaff] SOURCE3 16 7.0412 7.4096
+angle cd cc nc 71.000000 114.980006 ![gaff] SOURCE3 23 4.6219 5.3935
+angle h4 cc nc 49.999998 120.030002 ![gaff] SOURCE3 16 1.9828 2.3863
+angle h5 cd os 51.299999 116.330006 ![gaff] SOURCE3 12 2.1788 3.2919
+angle cc cd h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle h4 cd os 52.300000 111.890001 ![gaff] SOURCE3 61 1.5084 2.3500
+angle cc cd os 69.999999 120.299999 ![gaff] SOURCE3 64 3.4271 5.4354
+angle cd os cd 66.500002 109.170001 ![gaff] SOURCE3 12 6.7381 7.2529
+angle na c2 os 73.885003 112.565001 ! Calculated with empirical approach
+angle h5 c2 os 51.700000 116.110006 ! same as hc-c2-os
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cd nc X 4.750000 2 180.000005 ![gaff] statistiv value from parm94
+dihe X cc nc X 4.750000 2 180.000005 ![gaff] statistic value from parm94
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe cd os cd h4 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cc cd os cd 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cd os cd nc 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cd os cd h5 1.050000 2 180.000005 ! same as X -c2-os-X
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na cc nd 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd nd 1.100000 2 180.000005 ! Using default value
+impr h5 na c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 na 1.100000 2 180.000005 ! Using default value
+impr c2 c2 na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 nc cd os 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd os 1.100000 2 180.000005 ! Using default value
+impr cd h4 cc nc 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nc 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in non-pure aromatic systems
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw h5 0.015000 1.359000 0.015000 1.359000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 2 electrwd. group
+vdw os 0.170000 1.683700 0.170000 1.683700 8 16.000000 ![gaff] Ether and ester oxygen
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PCN N1 npx -0.05656 14.00670 N 7 0.000000 0.000000 0
+1 MAIN 1 PCN H1 hn 0.00000 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 PCN CP11 cpa 0.01736 12.01070 C 6 0.000000 0.000000 0
+3 MAIN 1 PCN CP12 cpb -0.17644 12.01070 C 6 0.000000 0.000000 0
+4 MAIN 1 PCN CP13 cpb -0.14031 12.01070 C 6 0.000000 0.000000 0
+5 MAIN 1 PCN CP14 cpa 0.00673 12.01070 C 6 0.000000 0.000000 0
+6 MAIN 1 PCN CA11 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 PCN HA11 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 PCN CA12 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 PCN HA12 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+10 MAIN 1 PCN CA13 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+11 MAIN 1 PCN HA13 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 PCN CA14 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 PCN HA14 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 PCN NM1 npm -0.02193 14.00670 N 7 0.000000 0.000000 0
+15 MAIN 1 PCN N2 npy -0.04347 14.00670 N 7 0.000000 0.000000 0
+16 MAIN 1 PCN CP21 cpa 0.01163 12.01070 C 6 0.000000 0.000000 0
+17 MAIN 1 PCN CP22 cpb -0.12395 12.01070 C 6 0.000000 0.000000 0
+18 MAIN 1 PCN CP23 cpb -0.17334 12.01070 C 6 0.000000 0.000000 0
+19 MAIN 1 PCN CP24 cpa 0.00242 12.01070 C 6 0.000000 0.000000 0
+20 MAIN 1 PCN CA21 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+21 MAIN 1 PCN HA21 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+22 MAIN 1 PCN CA22 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+23 MAIN 1 PCN HA22 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+24 MAIN 1 PCN CA23 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+25 MAIN 1 PCN HA23 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+26 MAIN 1 PCN CA24 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+27 MAIN 1 PCN HA24 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+28 MAIN 1 PCN NM2 npm -0.02780 14.00670 N 7 0.000000 0.000000 0
+29 MAIN 1 PCN N3 npx -0.04347 14.00670 N 7 0.000000 0.000000 0
+30 MAIN 1 PCN H3 hn 0.00000 1.00790 H 1 1.000000 0.000000 0
+31 MAIN 1 PCN CP31 cpa 0.00242 12.01070 C 6 0.000000 0.000000 0
+32 MAIN 1 PCN CP32 cpb -0.17334 12.01070 C 6 0.000000 0.000000 0
+33 MAIN 1 PCN CP33 cpb -0.12395 12.01070 C 6 0.000000 0.000000 0
+34 MAIN 1 PCN CP34 cpa 0.01163 12.01070 C 6 0.000000 0.000000 0
+35 MAIN 1 PCN CA31 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+36 MAIN 1 PCN HA31 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+37 MAIN 1 PCN CA32 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+38 MAIN 1 PCN HA32 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+39 MAIN 1 PCN CA33 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+40 MAIN 1 PCN HA33 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+41 MAIN 1 PCN CA34 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+42 MAIN 1 PCN HA34 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+43 MAIN 1 PCN NM3 npm -0.03562 14.00670 N 7 0.000000 0.000000 0
+44 MAIN 1 PCN N4 npy -0.05656 14.00670 N 7 0.000000 0.000000 0
+45 MAIN 1 PCN CP41 cpa 0.00673 12.01070 C 6 0.000000 0.000000 0
+46 MAIN 1 PCN CP42 cpb -0.14031 12.01070 C 6 0.000000 0.000000 0
+47 MAIN 1 PCN CP43 cpb -0.17644 12.01070 C 6 0.000000 0.000000 0
+48 MAIN 1 PCN CP44 cpa 0.01736 12.01070 C 6 0.000000 0.000000 0
+49 MAIN 1 PCN CA41 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+50 MAIN 1 PCN HA41 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+51 MAIN 1 PCN CA42 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+52 MAIN 1 PCN HA42 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+53 MAIN 1 PCN CA43 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+54 MAIN 1 PCN HA43 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+55 MAIN 1 PCN CA44 ca -0.12800 12.01070 C 6 1.000000 0.000000 0
+56 MAIN 1 PCN HA44 ha 0.12800 1.00790 H 1 1.000000 0.000000 0
+57 MAIN 1 PCN NM4 npm -0.02780 14.00670 N 7 0.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 1.42772584 -1.43745981 -0.00030187
+1 0.71377996 -0.71706107 0.00063913
+2 1.15394683 -2.78847294 -0.00289536
+3 2.44224599 -3.46124679 -0.00541418
+4 3.44487164 -2.46465534 -0.00101172
+5 2.78030975 -1.17268534 0.00084320
+6 2.77670201 -4.81842961 -0.01238859
+7 2.00045388 -5.57723596 -0.01758497
+8 4.12744899 -5.15427671 -0.01388621
+9 4.42031981 -6.20081246 -0.01964463
+10 5.12774147 -4.15980532 -0.00748088
+11 6.17244041 -4.45916271 -0.00866253
+12 4.80009183 -2.80716861 -0.00122561
+13 5.56239671 -2.03436294 0.00341696
+14 3.38196962 0.00000000 -0.00000000
+15 -1.38353098 -1.37399448 -0.00103882
+16 -2.73355440 -1.16850992 0.00207033
+17 -3.45751386 -2.44448699 0.01015522
+18 -2.46748284 -3.44088763 0.01199560
+19 -1.18668632 -2.72510842 0.00316592
+20 -4.81179822 -2.77103354 0.01641391
+21 -5.57164143 -1.99523103 0.01452273
+22 -5.15122431 -4.12655119 0.02551193
+23 -6.19852242 -4.41768815 0.03040514
+24 -4.16036604 -5.12374326 0.02859691
+25 -4.45839335 -6.16906964 0.03628219
+26 -2.80258469 -4.79292215 0.02171293
+27 -2.03141972 -5.55747437 0.02372139
+28 -0.02283252 -3.38192684 -0.00000061
+29 -1.42772606 1.43745934 0.00030000
+30 -0.71378107 0.71705941 -0.00064074
+31 -1.15394646 2.78847227 0.00289523
+32 -2.44224522 3.46124628 0.00541608
+33 -3.44487134 2.46465564 0.00101451
+34 -2.78030999 1.17268542 -0.00084181
+35 -2.77669999 4.81842907 0.01239086
+36 -2.00045144 5.57723474 0.01758632
+37 -4.12744657 5.15427745 0.01388998
+38 -4.42031664 6.20081337 0.01964881
+39 -5.12773986 4.15980692 0.00748559
+40 -6.17243865 4.45916492 0.00866836
+41 -4.80009129 2.80716990 0.00122978
+42 -5.56239702 2.03436490 -0.00341232
+43 -3.38197046 0.00000029 0.00000186
+44 1.38353133 1.37399468 0.00103969
+45 2.73355435 1.16851013 -0.00206950
+46 3.45751328 2.44448710 -0.01015639
+47 2.46748241 3.44088685 -0.01199779
+48 1.18668623 2.72510802 -0.00316684
+49 4.81179715 2.77103389 -0.01641631
+50 5.57164087 1.99523205 -0.01452428
+51 5.15122283 4.12655162 -0.02551646
+52 6.19852080 4.41768892 -0.03041061
+53 4.16036418 5.12374320 -0.02860255
+54 4.45839104 6.16906964 -0.03628965
+55 2.80258310 4.79292114 -0.02171759
+56 2.03141793 5.55747290 -0.02372691
+57 0.02283271 3.38192565 0.00000000
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 2 0 5 2 3 3 4
+4 5 5 14 15 16 15 19
+16 17 17 18 18 19 19 28
+29 31 29 34 31 32 32 33
+33 34 34 43 44 45 44 48
+45 46 46 47 47 48 48 57
+14 45 28 2 43 16 57 31
+29 30 0 1 6 7 6 8
+8 9 8 10 10 11 10 12
+12 13 3 6 12 4 20 21
+20 22 22 23 22 24 24 25
+24 26 26 27 17 20 18 26
+35 36 35 37 37 38 37 39
+39 40 39 41 41 42 32 35
+33 41 49 50 49 51 51 52
+51 53 53 54 53 55 55 56
+46 49 55 47
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 5 0 2 3 2 3 4
+3 4 5 0 5 4 0 5 14
+4 5 14 16 15 19 15 16 17
+16 17 18 17 18 19 15 19 18
+15 19 28 18 19 28 31 29 34
+29 31 32 31 32 33 32 33 34
+29 34 33 29 34 43 33 34 43
+45 44 48 44 45 46 45 46 47
+46 47 48 44 48 47 44 48 57
+47 48 57 5 14 45 14 45 44
+14 45 46 19 28 2 28 2 0
+28 2 3 34 43 16 43 16 15
+43 16 17 48 57 31 57 31 29
+57 31 32 31 29 30 34 29 30
+2 0 1 5 0 1 8 6 7
+6 8 9 6 8 10 10 8 9
+8 10 11 8 10 12 12 10 11
+10 12 13 2 3 6 4 3 6
+3 6 7 3 6 8 10 12 4
+13 12 4 12 4 3 12 4 5
+22 20 21 20 22 23 20 22 24
+24 22 23 22 24 25 22 24 26
+26 24 25 24 26 27 16 17 20
+18 17 20 17 20 21 17 20 22
+17 18 26 19 18 26 18 26 24
+18 26 27 37 35 36 35 37 38
+35 37 39 39 37 38 37 39 40
+37 39 41 41 39 40 39 41 42
+31 32 35 33 32 35 32 35 36
+32 35 37 32 33 41 34 33 41
+33 41 39 33 41 42 51 49 50
+49 51 52 49 51 53 53 51 52
+51 53 54 51 53 55 55 53 54
+53 55 56 45 46 49 47 46 49
+46 49 50 46 49 51 53 55 47
+56 55 47 55 47 46 55 47 48
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 0 2 3 2 0 5 4
+2 0 5 14 0 2 3 4
+2 3 4 5 3 4 5 0
+3 4 5 14 19 15 16 17
+16 15 19 18 16 15 19 28
+15 16 17 18 16 17 18 19
+17 18 19 15 17 18 19 28
+34 29 31 32 31 29 34 33
+31 29 34 43 29 31 32 33
+31 32 33 34 32 33 34 29
+32 33 34 43 48 44 45 46
+45 44 48 47 45 44 48 57
+44 45 46 47 45 46 47 48
+46 47 48 44 46 47 48 57
+5 14 45 44 5 14 45 46
+19 28 2 0 19 28 2 3
+34 43 16 15 34 43 16 17
+48 57 31 29 48 57 31 32
+5 0 2 28 28 2 3 4
+0 5 14 45 4 5 14 45
+19 15 16 43 43 16 17 18
+15 19 28 2 18 19 28 2
+34 29 31 57 57 31 32 33
+29 34 43 16 33 34 43 16
+48 44 45 14 14 45 46 47
+44 48 57 31 47 48 57 31
+1 0 2 3 1 0 2 28
+1 0 5 4 1 0 5 14
+30 29 31 32 30 29 31 57
+30 29 34 33 30 29 34 43
+7 6 8 9 7 6 8 10
+6 8 10 11 6 8 10 12
+9 8 10 11 9 8 10 12
+8 10 12 13 11 10 12 13
+2 3 6 7 2 3 6 8
+4 3 6 7 4 3 6 8
+10 12 4 3 10 12 4 5
+13 12 4 3 13 12 4 5
+21 20 22 23 21 20 22 24
+20 22 24 25 20 22 24 26
+23 22 24 25 23 22 24 26
+22 24 26 27 25 24 26 27
+16 17 20 21 16 17 20 22
+18 17 20 21 18 17 20 22
+17 18 26 24 17 18 26 27
+19 18 26 24 19 18 26 27
+36 35 37 38 36 35 37 39
+35 37 39 40 35 37 39 41
+38 37 39 40 38 37 39 41
+37 39 41 42 40 39 41 42
+31 32 35 36 31 32 35 37
+33 32 35 36 33 32 35 37
+32 33 41 39 32 33 41 42
+34 33 41 39 34 33 41 42
+50 49 51 52 50 49 51 53
+49 51 53 54 49 51 53 55
+52 51 53 54 52 51 53 55
+51 53 55 56 54 53 55 56
+45 46 49 50 45 46 49 51
+47 46 49 50 47 46 49 51
+53 55 47 46 53 55 47 48
+56 55 47 46 56 55 47 48
+0 2 3 6 28 2 3 6
+2 3 4 12 6 3 4 5
+6 3 4 12 12 4 5 0
+12 4 5 14 3 6 8 9
+3 6 8 10 8 10 12 4
+11 10 12 4 15 16 17 20
+43 16 17 20 16 17 18 26
+20 17 18 19 20 17 18 26
+26 18 19 15 26 18 19 28
+17 20 22 23 17 20 22 24
+22 24 26 18 25 24 26 18
+29 31 32 35 57 31 32 35
+31 32 33 41 35 32 33 34
+35 32 33 41 41 33 34 29
+41 33 34 43 32 35 37 38
+32 35 37 39 37 39 41 33
+40 39 41 33 44 45 46 49
+14 45 46 49 45 46 47 55
+49 46 47 48 49 46 47 55
+55 47 48 44 55 47 48 57
+46 49 51 52 46 49 51 53
+51 53 55 47 54 53 55 47
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+28 3 2 0 14 4 5 0
+43 17 16 15 28 18 19 15
+57 32 31 29 43 33 34 29
+14 46 45 44 57 47 48 44
+2 5 0 1 31 34 29 30
+2 4 3 6 3 5 4 12
+7 8 6 3 6 9 8 10
+8 11 10 12 10 13 12 4
+16 18 17 20 17 19 18 26
+21 22 20 17 20 23 22 24
+22 25 24 26 24 27 26 18
+31 33 32 35 32 34 33 41
+36 37 35 32 35 38 37 39
+37 40 39 41 39 42 41 33
+45 47 46 49 46 48 47 55
+50 51 49 46 49 52 51 53
+51 54 53 55 53 56 55 47
+
+!:md_parameters
+log_file ZnPor.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 565
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+bond Zn npx 199.999991 2.020000 ! [porphine3]
+bond cpa npx 459.999986 1.350000 ! [porphine3] bond order 1.06
+bond cpa cpb 427.000004 1.440000 ! [porphine3] bond order 1.14
+bond cpb cpb 469.000016 1.350000 ! [porphine3] bond order 1.65
+bond cpb ha 367.000001 1.060000 ! [porphine3]
+bond cpa cpm 455.000012 1.380000 ! [porphine3] bond order 1.31
+bond cpa npy 459.999986 1.350000 ! [porphine3]
+bond cp cpm 317.000016 1.500000 ! [porphine3] bond order 1.05
+bond Zn npy 199.999991 2.020000 ! [porphine3]
+bond cpm ha 367.000001 1.060000
+bond hn npx 406.600015 1.011000
+bond hn npy 406.600015 1.011000
+bond cpa npm 455.000012 1.380000
+bond ca cpb 478.399999 1.387000
+! type1 type2 type3 k a0
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+angle Zn npx cpa 80.000004 126.300006 ! [porphine3]
+angle cpa npx cpa 69.999999 106.800000 ! [porphine3]
+angle cpb cpa npx 69.999999 108.999997 ! [porphine3]
+angle cpa cpb cpb 69.999999 107.199997 ! [porphine3]
+angle cpa cpb ha 49.999998 125.099996 ! [porphine3]
+angle cpb cpb ha 49.999998 127.700003 ! [porphine3]
+angle cpm cpa npx 69.999999 125.999997 ! [porphine3]
+angle cpb cpa cpm 69.999999 124.800001 ! [porphine3]
+angle cpa npy cpa 69.999999 106.800000 ! [porphine3]
+angle cpb cpa npy 69.999999 108.999997 ! [porphine3]
+angle cpm cpa npy 69.999999 125.999997 ! [porphine3]
+angle cp cpm cpa 69.999999 117.799999 ! [porphine3]
+angle ca cp cpm 69.999999 120.000003 ! [porphine3]
+angle npx Zn npy 80.000004 90.000003 ! [porphine3]
+angle Zn npy cpa 80.000004 126.300006 ! [porphine3]
+angle npx Zn npx 80.000004 180.000005 ! [porphine3]
+angle npy Zn npy 80.000004 180.000005 ! [porphine3]
+angle cpa cpm cpa 69.999999 123.999994 ! [porphine3]
+angle cpa cpm ha 49.999998 117.500004
+angle cpa npx hn 49.999998 126.230010
+angle cpa npy hn 49.999998 126.230010
+angle ca cpb cpa 67.199999 119.970005
+angle ca cpb cpb 67.199999 119.970005
+angle cpb ca ha 48.499999 120.010003
+angle ca ca cpb 67.199999 119.970005
+angle npm cpa npx 69.999999 125.999997 ! [porphine3]
+angle cpb cpa npm 69.999999 124.800001 ! [porphine3]
+angle cpa npm cpa 69.999999 123.999994 ! [porphine3]
+angle npm cpa npy 69.999999 125.999997 ! [porphine3]
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+dihe X cpa npx X 2.400000 2 180.000005 ! [porphine3] bsd on HIS C=N
+dihe X cpb cpa X 5.150000 2 180.000005 ! [porphine3] bsd on HIS C=C
+dihe X cpb cpb X 5.150000 2 180.000005 ! [porphine3]
+dihe X cpa npy X 2.400000 2 180.000005 ! [porphine3]
+dihe X cpa cpm X 5.150000 2 180.000005 ! [porphine3]
+dihe X cpm cp X 0.500000 2 180.000005 ! [porphine3]
+dihe X npy Zn X 0.000000 2 180.000005 ! [porphine3]
+dihe X npx Zn X 0.000000 2 180.000005 ! [porphine3]
+dihe X npm cpa X 5.150000 2 180.000005
+dihe X cpb ca X 3.620000 2 180.000005
+! type1 type2 type3 type4 k periodicity phi0
+impr ha X ca X 1.100000 2 180.000005 ![gaff] bsd.on C6H6 nmodes
+impr X X Zn X 0.000000 2 180.000005 ! [porphine3]
+impr X X npx X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpa X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpb X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpm X 1.000000 2 180.000005 ! [porphine3]
+impr X X npy X 1.000000 2 180.000005 ! [porphine3]
+impr X X cp X 1.000000 2 180.000005 ! [porphine3]
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw hn 0.015700 0.600000 0.015700 0.600000 1 1.008000 ![gaff] H bonded to nitrogen atoms
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+vdw npx 0.238400 1.600013 0.238400 1.600013 0 0.000000 ! [porphine3] Porphyrin pyrrole-N
+vdw cpa 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin pyrrole-alpha
+vdw cpb 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin pyrrole-beta
+vdw cpm 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin meso
+vdw npy 0.238400 1.600013 0.238400 1.600013 0 0.000000 ! [porphine3] Porphyrin pyrrole-N
+vdw npm 0.238400 1.600013 0.238400 1.600013 0 0.000000 ! [porphine3] Porphyrin pyrrole-N
+
+!:velocity
+! idx vx vy vz
+0 -0.00085128 -0.00357234 0.00925774
+1 0.00000000 0.00000000 0.00000000
+2 -0.00551527 -0.00449193 -0.00231489
+3 -0.00098362 -0.00616697 -0.00073507
+4 0.00948409 0.00603226 -0.00671523
+5 -0.00212000 -0.00456446 0.00450640
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00528493 0.00723462 0.00671753
+15 0.00051893 0.00673376 -0.00334050
+16 -0.00535579 -0.00358755 -0.00075403
+17 0.00356379 0.00209334 0.00182132
+18 -0.00211497 0.00203511 -0.00220221
+19 0.00153342 0.00503496 -0.00789317
+20 0.00000000 0.00000000 0.00000000
+21 0.00000000 0.00000000 0.00000000
+22 0.00000000 0.00000000 0.00000000
+23 0.00000000 0.00000000 0.00000000
+24 0.00000000 0.00000000 0.00000000
+25 0.00000000 0.00000000 0.00000000
+26 0.00000000 0.00000000 0.00000000
+27 0.00000000 0.00000000 0.00000000
+28 -0.00094121 -0.00078133 0.00313763
+29 0.00357452 0.00434949 0.00100529
+30 0.00000000 0.00000000 0.00000000
+31 -0.00018702 0.00017791 -0.00297618
+32 -0.00043391 -0.00122197 0.00687172
+33 -0.00115067 0.00461534 0.00958334
+34 0.00508387 -0.00427770 0.00330633
+35 0.00000000 0.00000000 0.00000000
+36 0.00000000 0.00000000 0.00000000
+37 0.00000000 0.00000000 0.00000000
+38 0.00000000 0.00000000 0.00000000
+39 0.00000000 0.00000000 0.00000000
+40 0.00000000 0.00000000 0.00000000
+41 0.00000000 0.00000000 0.00000000
+42 0.00000000 0.00000000 0.00000000
+43 0.00472525 0.00168816 0.00279377
+44 0.00186045 -0.00483712 0.00671377
+45 -0.00111072 -0.00345112 -0.00053918
+46 -0.00304124 -0.00530515 -0.00526337
+47 -0.00207110 0.00448664 -0.00221449
+48 -0.00332123 0.00024460 0.00124331
+49 0.00000000 0.00000000 0.00000000
+50 0.00000000 0.00000000 0.00000000
+51 0.00000000 0.00000000 0.00000000
+52 0.00000000 0.00000000 0.00000000
+53 0.00000000 0.00000000 0.00000000
+54 0.00000000 0.00000000 0.00000000
+55 0.00000000 0.00000000 0.00000000
+56 0.00000000 0.00000000 0.00000000
+57 -0.00204963 -0.00616710 0.00572731
+
+!:force
+! idx fx fy fz
+0 -0.01286961 0.03147501 0.00937431
+1 0.00000000 0.00000000 0.00000000
+2 0.00823492 -0.02819368 -0.00299923
+3 -0.00723488 -0.01781106 0.00613144
+4 -0.00701899 -0.00063565 -0.00842360
+5 0.01918894 0.00385963 -0.00256507
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 -0.00168599 -0.01817334 -0.00354987
+15 -0.03368430 -0.01613609 -0.00333577
+16 0.03086813 0.02062345 0.00918021
+17 0.00893704 -0.00457646 -0.00034531
+18 -0.00550398 0.00461192 0.00234644
+19 0.03414927 0.00319719 -0.00667542
+20 0.00000000 0.00000000 0.00000000
+21 0.00000000 0.00000000 0.00000000
+22 0.00000000 0.00000000 0.00000000
+23 0.00000000 0.00000000 0.00000000
+24 0.00000000 0.00000000 0.00000000
+25 0.00000000 0.00000000 0.00000000
+26 0.00000000 0.00000000 0.00000000
+27 0.00000000 0.00000000 0.00000000
+28 -0.00308737 0.00728870 -0.00629586
+29 -0.00475063 0.01408641 -0.00478516
+30 0.00000000 0.00000000 0.00000000
+31 0.01903859 0.00958797 0.00719568
+32 -0.02706312 -0.00683203 0.00191163
+33 0.02322472 0.01885905 0.01948181
+34 -0.01959851 -0.00696685 0.00207076
+35 0.00000000 0.00000000 0.00000000
+36 0.00000000 0.00000000 0.00000000
+37 0.00000000 0.00000000 0.00000000
+38 0.00000000 0.00000000 0.00000000
+39 0.00000000 0.00000000 0.00000000
+40 0.00000000 0.00000000 0.00000000
+41 0.00000000 0.00000000 0.00000000
+42 0.00000000 0.00000000 0.00000000
+43 -0.00732674 -0.01192423 -0.01072069
+44 0.00953170 0.01594649 0.00184764
+45 -0.02214308 -0.00614316 -0.00035499
+46 0.02714149 0.00499208 0.00239379
+47 -0.01341513 0.00136434 0.00672261
+48 -0.02311692 -0.01785024 0.00639588
+49 0.00000000 0.00000000 0.00000000
+50 0.00000000 0.00000000 0.00000000
+51 0.00000000 0.00000000 0.00000000
+52 0.00000000 0.00000000 0.00000000
+53 0.00000000 0.00000000 0.00000000
+54 0.00000000 0.00000000 0.00000000
+55 0.00000000 0.00000000 0.00000000
+56 0.00000000 0.00000000 0.00000000
+57 0.02421429 -0.00344708 -0.01104512
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.114162
+-0.000000 0.000000 0.000000
+38.276825 0.181896 -0.006351 -0.983297
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 POR N1 npx -0.25297 14.00670 N 7 0.000000 0.000000 0
+1 MAIN 1 POR H1 hn 0.20488 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 POR CP11 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+3 MAIN 1 POR CP12 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+4 MAIN 1 POR HP12 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+5 MAIN 1 POR CP13 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+6 MAIN 1 POR HP13 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+7 MAIN 1 POR CP14 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+8 MAIN 1 POR CM1 cpm -0.19683 12.01070 C 6 0.000000 0.000000 0
+9 MAIN 1 POR HM1 ha 0.12468 1.00790 H 1 1.000000 0.000000 0
+10 MAIN 1 POR N2 npy -0.25297 14.00670 N 7 0.000000 0.000000 0
+11 MAIN 1 POR CP21 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+12 MAIN 1 POR CP22 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+13 MAIN 1 POR HP22 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+14 MAIN 1 POR CP23 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+15 MAIN 1 POR HP23 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+16 MAIN 1 POR CP24 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+17 MAIN 1 POR CM2 cpm -0.19683 12.01070 C 6 0.000000 0.000000 0
+18 MAIN 1 POR HM2 ha 0.12468 1.00790 H 1 1.000000 0.000000 0
+19 MAIN 1 POR N3 npx -0.25297 14.00670 N 7 0.000000 0.000000 0
+20 MAIN 1 POR H3 hn 0.20488 1.00790 H 1 1.000000 0.000000 0
+21 MAIN 1 POR CP31 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+22 MAIN 1 POR CP32 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+23 MAIN 1 POR HP32 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+24 MAIN 1 POR CP33 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+25 MAIN 1 POR HP33 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+26 MAIN 1 POR CP34 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+27 MAIN 1 POR CM3 cpm -0.19683 12.01070 C 6 0.000000 0.000000 0
+28 MAIN 1 POR HM3 ha 0.12468 1.00790 H 1 1.000000 0.000000 0
+29 MAIN 1 POR N4 npy -0.25297 14.00670 N 7 0.000000 0.000000 0
+30 MAIN 1 POR CP41 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+31 MAIN 1 POR CP42 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+32 MAIN 1 POR HP42 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+33 MAIN 1 POR CP43 cpb -0.18672 12.01070 C 6 0.000000 0.000000 0
+34 MAIN 1 POR HP43 ha 0.14083 1.00790 H 1 0.000000 0.000000 0
+35 MAIN 1 POR CP44 cpa 0.15722 12.01070 C 6 0.000000 0.000000 0
+36 MAIN 1 POR CM4 cpm -0.19683 12.01070 C 6 0.000000 0.000000 0
+37 MAIN 1 POR HM4 ha 0.12468 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 1.49283957 -1.50187939 -0.00102441
+1 0.77983999 -0.77858609 -0.00340277
+2 1.23754302 -2.85078772 -0.00059371
+3 2.51395067 -3.50767447 0.00074122
+4 2.64690605 -4.58183908 0.00178959
+5 3.48892266 -2.54189809 0.00131650
+6 4.56185992 -2.68476689 0.00302591
+7 2.84414598 -1.25986751 -0.00017790
+8 3.44133201 -0.00000000 0.00000000
+9 4.52786418 0.01126265 0.00117697
+10 -1.44279852 -1.42892057 0.00018874
+11 -2.79360350 -1.24143691 0.00047041
+12 -3.50201697 -2.51873455 0.00144694
+13 -4.57898451 -2.63886868 0.00152204
+14 -2.54584974 -3.48111626 0.00194872
+15 -2.67253378 -4.55729379 0.00264928
+16 -1.26408927 -2.78077110 0.00083759
+17 -0.02729684 -3.43737919 -0.00000158
+18 -0.04555623 -4.52381112 0.00052596
+19 -1.49283985 1.50187943 0.00102427
+20 -0.77984020 0.77858575 0.00340391
+21 -1.23754299 2.85078764 0.00059172
+22 -2.51395044 3.50767459 -0.00074466
+23 -2.64690548 4.58183917 -0.00179464
+24 -3.48892273 2.54189860 -0.00131816
+25 -4.56185995 2.68476773 -0.00302789
+26 -2.84414634 1.25986781 0.00017834
+27 -3.44133192 0.00000007 0.00000174
+28 -4.52786414 -0.01126306 -0.00117357
+29 1.44279919 1.42892050 -0.00018880
+30 2.79360416 1.24143709 -0.00046812
+31 3.50201677 2.51873496 -0.00144353
+32 4.57898412 2.63886933 -0.00151745
+33 2.54584916 3.48111605 -0.00194727
+34 2.67253287 4.55729354 -0.00264757
+35 1.26408907 2.78077051 -0.00083808
+36 0.02729681 3.43737851 0.00000000
+37 0.04555673 4.52381033 -0.00052909
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 2 0 7 2 3 3 5
+3 4 5 7 5 6 7 8
+10 11 10 16 11 12 12 14
+12 13 14 16 14 15 16 17
+19 21 19 26 21 22 22 24
+22 23 24 26 24 25 26 27
+29 30 29 35 30 31 31 33
+31 32 33 35 33 34 35 36
+8 30 17 2 27 11 36 21
+36 37 27 28 17 18 8 9
+19 20 0 1
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 7 0 2 3 2 3 5
+2 3 4 5 3 4 3 5 7
+3 5 6 7 5 6 0 7 5
+0 7 8 5 7 8 11 10 16
+10 11 12 11 12 14 11 12 13
+14 12 13 12 14 16 12 14 15
+16 14 15 10 16 14 10 16 17
+14 16 17 21 19 26 19 21 22
+21 22 24 21 22 23 24 22 23
+22 24 26 22 24 25 26 24 25
+19 26 24 19 26 27 24 26 27
+30 29 35 29 30 31 30 31 33
+30 31 32 33 31 32 31 33 35
+31 33 34 35 33 34 29 35 33
+29 35 36 33 35 36 7 8 30
+8 30 29 8 30 31 16 17 2
+17 2 0 17 2 3 26 27 11
+27 11 10 27 11 12 35 36 21
+36 21 19 36 21 22 35 36 37
+21 36 37 26 27 28 11 27 28
+16 17 18 2 17 18 7 8 9
+30 8 9 21 19 20 26 19 20
+2 0 1 7 0 1
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+7 0 2 3 2 0 7 5
+2 0 7 8 0 2 3 5
+0 2 3 4 2 3 5 7
+2 3 5 6 4 3 5 7
+4 3 5 6 3 5 7 0
+3 5 7 8 6 5 7 0
+6 5 7 8 16 10 11 12
+11 10 16 14 11 10 16 17
+10 11 12 14 10 11 12 13
+11 12 14 16 11 12 14 15
+13 12 14 16 13 12 14 15
+12 14 16 10 12 14 16 17
+15 14 16 10 15 14 16 17
+26 19 21 22 21 19 26 24
+21 19 26 27 19 21 22 24
+19 21 22 23 21 22 24 26
+21 22 24 25 23 22 24 26
+23 22 24 25 22 24 26 19
+22 24 26 27 25 24 26 19
+25 24 26 27 35 29 30 31
+30 29 35 33 30 29 35 36
+29 30 31 33 29 30 31 32
+30 31 33 35 30 31 33 34
+32 31 33 35 32 31 33 34
+31 33 35 29 31 33 35 36
+34 33 35 29 34 33 35 36
+7 8 30 29 7 8 30 31
+16 17 2 0 16 17 2 3
+26 27 11 10 26 27 11 12
+35 36 21 19 35 36 21 22
+7 0 2 17 17 2 3 5
+17 2 3 4 0 7 8 30
+5 7 8 30 16 10 11 27
+27 11 12 14 27 11 12 13
+10 16 17 2 14 16 17 2
+26 19 21 36 36 21 22 24
+36 21 22 23 19 26 27 11
+24 26 27 11 35 29 30 8
+8 30 31 33 8 30 31 32
+29 35 36 21 33 35 36 21
+0 2 17 18 3 2 17 18
+0 7 8 9 5 7 8 9
+9 8 30 29 9 8 30 31
+10 11 27 28 12 11 27 28
+10 16 17 18 14 16 17 18
+19 21 36 37 22 21 36 37
+19 26 27 28 24 26 27 28
+29 35 36 37 33 35 36 37
+1 0 2 3 1 0 2 17
+1 0 7 5 1 0 7 8
+20 19 21 22 20 19 21 36
+20 19 26 24 20 19 26 27
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+17 3 2 0 4 2 3 5
+6 7 5 3 8 5 7 0
+27 12 11 10 13 11 12 14
+15 16 14 12 17 14 16 10
+36 22 21 19 23 21 22 24
+25 26 24 22 27 24 26 19
+8 31 30 29 32 30 31 33
+34 35 33 31 36 33 35 29
+7 30 8 9 16 2 17 18
+26 11 27 28 35 21 36 37
+2 7 0 1 21 26 19 20
+
+!:md_parameters
+log_file ZnPor.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 565
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond Zn npx 199.999991 2.020000 ! [porphine3]
+bond cpa npx 459.999986 1.350000 ! [porphine3] bond order 1.06
+bond cpa cpb 427.000004 1.440000 ! [porphine3] bond order 1.14
+bond cpb cpb 469.000016 1.350000 ! [porphine3] bond order 1.65
+bond cpb ha 367.000001 1.060000 ! [porphine3]
+bond cpa cpm 455.000012 1.380000 ! [porphine3] bond order 1.31
+bond cpa npy 459.999986 1.350000 ! [porphine3]
+bond cp cpm 317.000016 1.500000 ! [porphine3] bond order 1.05
+bond Zn npy 199.999991 2.020000 ! [porphine3]
+bond cpm ha 367.000001 1.060000
+bond hn npx 406.600015 1.011000
+bond hn npy 406.600015 1.011000
+! type1 type2 type3 k a0
+angle Zn npx cpa 80.000004 126.300006 ! [porphine3]
+angle cpa npx cpa 69.999999 106.800000 ! [porphine3]
+angle cpb cpa npx 69.999999 108.999997 ! [porphine3]
+angle cpa cpb cpb 69.999999 107.199997 ! [porphine3]
+angle cpa cpb ha 49.999998 125.099996 ! [porphine3]
+angle cpb cpb ha 49.999998 127.700003 ! [porphine3]
+angle cpm cpa npx 69.999999 125.999997 ! [porphine3]
+angle cpb cpa cpm 69.999999 124.800001 ! [porphine3]
+angle cpa npy cpa 69.999999 106.800000 ! [porphine3]
+angle cpb cpa npy 69.999999 108.999997 ! [porphine3]
+angle cpm cpa npy 69.999999 125.999997 ! [porphine3]
+angle cp cpm cpa 69.999999 117.799999 ! [porphine3]
+angle ca cp cpm 69.999999 120.000003 ! [porphine3]
+angle npx Zn npy 80.000004 90.000003 ! [porphine3]
+angle Zn npy cpa 80.000004 126.300006 ! [porphine3]
+angle npx Zn npx 80.000004 180.000005 ! [porphine3]
+angle npy Zn npy 80.000004 180.000005 ! [porphine3]
+angle cpa cpm cpa 69.999999 123.999994 ! [porphine3]
+angle cpa cpm ha 49.999998 117.500004
+angle cpa npx hn 49.999998 126.230010
+angle cpa npy hn 49.999998 126.230010
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cpa npx X 2.400000 2 180.000005 ! [porphine3] bsd on HIS C=N
+dihe X cpb cpa X 5.150000 2 180.000005 ! [porphine3] bsd on HIS C=C
+dihe X cpb cpb X 5.150000 2 180.000005 ! [porphine3]
+dihe X cpa npy X 2.400000 2 180.000005 ! [porphine3]
+dihe X cpa cpm X 5.150000 2 180.000005 ! [porphine3]
+dihe X cpm cp X 0.500000 2 180.000005 ! [porphine3]
+dihe X npy Zn X 0.000000 2 180.000005 ! [porphine3]
+dihe X npx Zn X 0.000000 2 180.000005 ! [porphine3]
+! type1 type2 type3 type4 k periodicity phi0
+impr X X Zn X 0.000000 2 180.000005 ! [porphine3]
+impr X X npx X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpa X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpb X 1.000000 2 180.000005 ! [porphine3]
+impr X X cpm X 1.000000 2 180.000005 ! [porphine3]
+impr X X npy X 1.000000 2 180.000005 ! [porphine3]
+impr X X cp X 1.000000 2 180.000005 ! [porphine3]
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw hn 0.015700 0.600000 0.015700 0.600000 1 1.008000 ![gaff] H bonded to nitrogen atoms
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+vdw npx 0.238400 1.600013 0.238400 1.600013 0 0.000000 ! [porphine3] Porphyrin pyrrole-N
+vdw cpa 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin pyrrole-alpha
+vdw cpb 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin pyrrole-beta
+vdw cpm 0.086000 1.908017 0.086000 1.908017 0 0.000000 ! [porphine3] Porphyrin meso
+vdw npy 0.238400 1.600013 0.238400 1.600013 0 0.000000 ! [porphine3] Porphyrin pyrrole-N
+
+!:velocity
+! idx vx vy vz
+0 -0.00085128 -0.00357234 0.00925774
+1 0.00000000 0.00000000 0.00000000
+2 -0.00551527 -0.00449193 -0.00231489
+3 -0.00098362 -0.00616697 -0.00073507
+4 0.00137781 -0.00423328 0.00010141
+5 0.00948409 0.00603226 -0.00671523
+6 0.01137363 0.00372444 0.00345894
+7 -0.00212000 -0.00456446 0.00450640
+8 0.00528493 0.00723462 0.00671753
+9 0.00000000 0.00000000 0.00000000
+10 0.00051893 0.00673376 -0.00334050
+11 -0.00535579 -0.00358755 -0.00075403
+12 0.00356379 0.00209334 0.00182132
+13 0.00644938 -0.00485489 -0.01055128
+14 -0.00211497 0.00203511 -0.00220221
+15 -0.01214494 -0.00071840 0.01796844
+16 0.00153342 0.00503496 -0.00789317
+17 -0.00094121 -0.00078133 0.00313763
+18 0.00000000 0.00000000 0.00000000
+19 0.00357452 0.00434949 0.00100529
+20 0.00000000 0.00000000 0.00000000
+21 -0.00018702 0.00017791 -0.00297618
+22 -0.00043391 -0.00122197 0.00687172
+23 -0.02324863 -0.01158874 0.02802984
+24 -0.00115067 0.00461534 0.00958334
+25 0.00302621 0.02906800 -0.01553263
+26 0.00508387 -0.00427770 0.00330633
+27 0.00472525 0.00168816 0.00279377
+28 0.00000000 0.00000000 0.00000000
+29 0.00186045 -0.00483712 0.00671377
+30 -0.00111072 -0.00345112 -0.00053918
+31 -0.00304124 -0.00530515 -0.00526337
+32 -0.00660958 -0.01696974 0.00419765
+33 -0.00207110 0.00448664 -0.00221449
+34 0.00522417 -0.02145727 0.00918572
+35 -0.00332123 0.00024460 0.00124331
+36 -0.00204963 -0.00616710 0.00572731
+37 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 -0.01286961 0.03147501 0.00937431
+1 0.00000000 0.00000000 0.00000000
+2 0.00823492 -0.02819368 -0.00299923
+3 -0.00723488 -0.01781106 0.00613144
+4 0.00441888 0.00521204 -0.00419223
+5 -0.00701899 -0.00063565 -0.00842360
+6 0.00938990 0.00540532 0.00249857
+7 0.01918894 0.00385963 -0.00256507
+8 -0.00168599 -0.01817334 -0.00354987
+9 0.00000000 0.00000000 0.00000000
+10 -0.03368430 -0.01613609 -0.00333577
+11 0.03086813 0.02062345 0.00918021
+12 0.00893704 -0.00457646 -0.00034531
+13 -0.01569323 -0.01023713 -0.00109299
+14 -0.00550398 0.00461192 0.00234644
+15 -0.00136076 0.00011571 0.00041788
+16 0.03414927 0.00319719 -0.00667542
+17 -0.00308737 0.00728870 -0.00629586
+18 0.00000000 0.00000000 0.00000000
+19 -0.00475063 0.01408641 -0.00478516
+20 0.00000000 0.00000000 0.00000000
+21 0.01903859 0.00958797 0.00719568
+22 -0.02706312 -0.00683203 0.00191163
+23 0.01555710 -0.00274391 -0.01067324
+24 0.02322472 0.01885905 0.01948181
+25 -0.00582034 -0.01279221 -0.00697177
+26 -0.01959851 -0.00696685 0.00207076
+27 -0.00732674 -0.01192423 -0.01072069
+28 0.00000000 0.00000000 0.00000000
+29 0.00953170 0.01594649 0.00184764
+30 -0.02214308 -0.00614316 -0.00035499
+31 0.02714149 0.00499208 0.00239379
+32 -0.00619047 0.00539550 -0.00041097
+33 -0.01341513 0.00136434 0.00672261
+34 0.00146379 -0.00800365 -0.00697266
+35 -0.02311692 -0.01785024 0.00639588
+36 0.02421429 -0.00344708 -0.01104512
+37 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.269080
+-0.000000 0.000000 0.000000
+94.383492 -0.075632 0.002134 0.997133
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PYR N1 nb -0.44876 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PYR C2 ca 0.15519 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 PYR H2 h4 0.06919 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 PYR C3 ca 0.15519 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 PYR H3 h4 0.06919 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 PYR N4 nb -0.44876 14.00670 N 7 1.000000 0.000000 0
+6 MAIN 1 PYR C5 ca 0.15519 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 PYR H5 h4 0.06919 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 PYR C6 ca 0.15519 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 PYR H6 h4 0.06919 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.65640752 0.58789748 -1.07233300
+1 0.65886163 0.58854106 -0.97666219
+2 1.21161267 1.06353178 -1.76667197
+3 1.31166180 0.00252394 0.09623639
+4 2.38450964 0.01062579 0.16102348
+5 0.64955820 -0.58446493 1.07406522
+6 -0.66571095 -0.58510856 0.97839438
+7 -1.21846195 -1.06010025 1.76840360
+8 -1.31851114 0.00090901 -0.09450395
+9 -2.39135900 -0.00719225 -0.15929070
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 8 1 2 1 3
+3 4 3 5 5 6 6 7
+6 8 8 9
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+8 0 1 0 1 2 0 1 3
+0 8 6 0 8 9 3 1 2
+1 3 4 1 3 5 5 3 4
+3 5 6 5 6 7 5 6 8
+8 6 7 6 8 9
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+8 0 1 2 8 0 1 3
+1 0 8 6 1 0 8 9
+0 1 3 4 0 1 3 5
+2 1 3 4 2 1 3 5
+1 3 5 6 4 3 5 6
+3 5 6 7 3 5 6 8
+5 6 8 0 5 6 8 9
+7 6 8 0 7 6 8 9
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 4 3 5 5 7 6 8
+0 2 1 3 0 6 8 9
+
+!:md_parameters
+log_file pyridine.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 7
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca nb 483.099991 1.342000 ![gaff] SOURCE3 104 0.0052 0.0076
+bond ca h4 342.900008 1.088000 ![gaff] SOURCE3 57 0.0016 0.0026
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+! type1 type2 type3 k a0
+angle ca nb ca 68.599997 115.860007 ![gaff] SOURCE3 46 0.9817 1.1645
+angle h4 ca nb 51.800001 115.940002 ![gaff] SOURCE3 52 0.5536 0.7370
+angle ca ca nb 69.199996 122.629995 ![gaff] SOURCE3 83 0.9345 1.1249
+angle ca ca h4 48.199999 121.089992 ![gaff] SOURCE3 57 1.0923 1.4696
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca nb X 4.800000 2 180.000005 ![gaff] same as X-CA-NC-X
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+! type1 type2 type3 type4 k periodicity phi0
+impr ca h4 ca nb 1.100000 2 180.000005 ! Using default value
+impr ca ca ca ha 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nb 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in pure aromatic systems
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+57.683319 0.984367 0.125721 -0.123357
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PRZ N1 na -0.02451 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PRZ H1 hn 0.30350 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 PRZ N2 nc -0.46249 14.00670 N 7 1.000000 0.000000 0
+3 MAIN 1 PRZ C3 cd 0.12267 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 PRZ H3 h4 0.12865 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 PRZ C4 cd -0.28193 12.01070 C 6 1.000000 0.000000 0
+6 MAIN 1 PRZ H4 ha 0.16369 1.00790 H 1 1.000000 0.000000 0
+7 MAIN 1 PRZ C5 cc -0.12007 12.01070 C 6 1.000000 0.000000 0
+8 MAIN 1 PRZ H5 h4 0.17049 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.68729807 0.61905549 -1.12911167
+1 -1.07859847 1.05937252 -1.92809140
+2 0.63456400 0.59244454 -0.98525593
+3 0.83765340 -0.03959967 0.13522716
+4 1.83660027 -0.19870580 0.48706362
+5 -0.37666897 -0.43610591 0.73937882
+6 -0.51844358 -0.96662192 1.65688715
+7 -1.33300611 0.01530876 -0.12060898
+8 -2.40080996 -0.04567733 -0.09254202
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 7 2 3
+3 4 5 6 5 7 7 8
+5 3
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 7 0 1 7 0 2
+0 2 3 0 7 5 0 7 8
+2 3 4 7 5 6 5 7 8
+6 5 3 7 5 3 5 3 2
+5 3 4
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 7 0 2 3
+1 0 7 5 1 0 7 8
+2 0 7 5 2 0 7 8
+0 2 3 4 6 5 7 0
+6 5 7 8 6 5 3 2
+6 5 3 4 7 5 3 2
+7 5 3 4 0 2 3 5
+3 5 7 0 3 5 7 8
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 2 0 7 2 4 3 5
+6 7 5 3 0 5 7 8
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 11
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond hn na 406.600015 1.011000 ![gaff] SOURCE3 46 0.0076 0.0107
+bond na nc 535.700021 1.350000 ![gaff] SOURCE3 152 0.0117 0.0180
+bond cc na 438.799985 1.371000 ![gaff] SOURCE3 440 0.0107 0.0144
+bond cd nc 494.599991 1.335000 ![gaff] SOURCE3 203 0.0171 0.0239
+bond cd h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cd ha 347.200012 1.085000 ![gaff] SOURCE3 740 0.0029 0.0039
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cd cd 418.299991 1.429000 ![gaff] SOURCE1 740 0.0058 0.0069
+! type1 type2 type3 k a0
+angle hn na nc 49.999998 119.610000 ![gaff] SOURCE3 16 1.4674 1.8079
+angle cc na hn 47.200002 124.660009 ![gaff] SOURCE3 38 4.3279 5.9689
+angle cc na nc 70.199997 113.019994 ![gaff] SOURCE3 38 1.6684 2.2867
+angle cd nc na 74.199996 103.730001 ![gaff] SOURCE3 122 1.9430 2.3292
+angle cd cc na 72.900000 109.419999 ![gaff] SOURCE3 265 1.3410 2.6051
+angle h4 cc na 50.200001 119.660010 ![gaff] SOURCE3 294 0.9445 2.4702
+angle h4 cd nc 51.400000 119.110002 ![gaff] SOURCE3 135 1.2486 1.6946
+angle cc cd ha 48.400002 122.889993 ![gaff] SOURCE3 584 2.3225 2.9334
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cd cd ha 46.599998 123.739996 ![gaff] SOURCE3 656 2.7165 3.3195
+angle cc cd cd 68.199995 114.190005 ![gaff] SOURCE3 517 5.4334 6.5960
+angle cd cd nc 71.099997 112.559994 ![gaff] SOURCE3 141 3.3765 4.2871
+angle cd cd h4 45.599997 129.470006 ![gaff] SOURCE3 171 1.7718 2.2734
+! type1 type2 type3 type4 k periodicity phi0
+dihe X na nc X 4.800000 2 180.000005 ![gaff] estimated, intrpol.
+dihe X cc na X 1.700000 2 180.000005 ![gaff] statistic value from parm94
+dihe X cd nc X 4.750000 2 180.000005 ![gaff] statistiv value from parm94
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe X cd cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr cd h4 cd nc 1.100000 2 180.000005 ! Using default value
+impr cc hn na nc 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw na 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N with three connected atoms
+vdw hn 0.015700 0.600000 0.015700 0.600000 1 1.008000 ![gaff] H bonded to nitrogen atoms
+vdw nc 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in non-pure aromatic systems
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PRD N1 nb -0.32136 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PRD N2 nb -0.32136 14.00670 N 7 1.000000 0.000000 0
+2 MAIN 1 PRD C3 ca 0.33459 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 PRD H3 h4 0.02108 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 PRD C4 ca -0.17003 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 PRD H4 ha 0.13571 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 PRD C5 ca -0.17003 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 PRD H5 ha 0.13571 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 PRD C6 ca 0.33459 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 PRD H6 h4 0.02108 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.60005125 0.56606979 -1.03001089
+1 0.70768085 0.58218264 -0.96194677
+2 1.31782638 0.02614056 0.05539177
+3 2.39056178 0.08179109 0.03701584
+4 0.64373823 -0.60083601 1.10227055
+5 1.18432685 -1.04434398 1.91768435
+6 -0.72166556 -0.61765952 1.03120470
+7 -1.33291040 -1.07535934 1.78666857
+8 -1.29865030 -0.00609749 -0.08078906
+9 -2.36472562 0.02320036 -0.21048453
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 8 1 2 2 3
+2 4 4 5 4 6 6 7
+6 8 8 9
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+8 0 1 0 1 2 0 8 6
+0 8 9 1 2 3 1 2 4
+4 2 3 2 4 5 2 4 6
+6 4 5 4 6 7 4 6 8
+8 6 7 6 8 9
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+8 0 1 2 1 0 8 6
+1 0 8 9 0 1 2 3
+0 1 2 4 1 2 4 5
+1 2 4 6 3 2 4 5
+3 2 4 6 2 4 6 7
+2 4 6 8 5 4 6 7
+5 4 6 8 4 6 8 0
+4 6 8 9 7 6 8 0
+7 6 8 9
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 3 2 4 2 5 4 6
+4 7 6 8 0 6 8 9
+
+!:md_parameters
+log_file pyridine.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 7
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond nb nb 550.200019 1.342000 ![gaff] SOURCE1 15 0.0307 0.0314
+bond ca nb 483.099991 1.342000 ![gaff] SOURCE3 104 0.0052 0.0076
+bond ca h4 342.900008 1.088000 ![gaff] SOURCE3 57 0.0016 0.0026
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+! type1 type2 type3 k a0
+angle ca nb nb 69.400004 118.890002 ![gaff] SOURCE3 10 0.4394 0.6031
+angle ca ca nb 69.199996 122.629995 ![gaff] SOURCE3 83 0.9345 1.1249
+angle h4 ca nb 51.800001 115.940002 ![gaff] SOURCE3 52 0.5536 0.7370
+angle ca ca h4 48.199999 121.089992 ![gaff] SOURCE3 57 1.0923 1.4696
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca nb X 4.800000 2 180.000005 ![gaff] same as X-CA-NC-X
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+dihe ca nb nb ca 2.800000 1 0.000000 ! same as X -n2-n2-X
+! type1 type2 type3 type4 k periodicity phi0
+impr ca h4 ca nb 1.100000 2 180.000005 ! Using default value
+impr ca ca ca ha 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nb 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in pure aromatic systems
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+67.177032 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PYR N1 nb -0.57876 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PYR C2 ca 0.31160 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 PYR H2 h4 0.06114 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 PYR C3 ca -0.29196 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 PYR H3 ha 0.13721 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 PYR C4 ca 0.00992 12.01070 C 6 1.000000 0.000000 0
+6 MAIN 1 PYR H4 ha 0.13287 1.00790 H 1 1.000000 0.000000 0
+7 MAIN 1 PYR C5 ca -0.29196 12.01070 C 6 1.000000 0.000000 0
+8 MAIN 1 PYR H5 ha 0.13721 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 PYR C6 ca 0.31160 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 PYR H6 h4 0.06114 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.64634871 0.57886819 -1.05580188
+1 0.67187136 0.58608566 -0.97141234
+2 1.19566956 1.06918343 -1.77773258
+3 1.37618651 0.01652361 0.07650270
+4 2.44976481 0.05275742 0.09214530
+5 0.65993164 -0.59377556 1.09111415
+6 1.16650514 -1.04852355 1.92368565
+7 -0.72157102 -0.60688489 1.01236762
+8 -1.32177656 -1.06806495 1.77472857
+9 -1.32093991 -0.00613354 -0.08236587
+10 -2.39280759 0.00276916 -0.17681613
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 9 1 2 1 3
+3 4 3 5 5 6 5 7
+7 8 7 9 9 10
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+9 0 1 0 1 2 0 1 3
+0 9 7 0 9 10 3 1 2
+1 3 4 1 3 5 5 3 4
+3 5 6 3 5 7 7 5 6
+5 7 8 5 7 9 9 7 8
+7 9 10
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+9 0 1 2 9 0 1 3
+1 0 9 7 1 0 9 10
+0 1 3 4 0 1 3 5
+2 1 3 4 2 1 3 5
+1 3 5 6 1 3 5 7
+4 3 5 6 4 3 5 7
+3 5 7 8 3 5 7 9
+6 5 7 8 6 5 7 9
+5 7 9 0 5 7 9 10
+8 7 9 0 8 7 9 10
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 4 3 5 3 6 5 7
+5 8 7 9 0 2 1 3
+0 7 9 10
+
+!:md_parameters
+log_file (null)
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 4
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca nb 483.099991 1.342000 ![gaff] SOURCE3 104 0.0052 0.0076
+bond ca h4 342.900008 1.088000 ![gaff] SOURCE3 57 0.0016 0.0026
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+! type1 type2 type3 k a0
+angle ca nb ca 68.599997 115.860007 ![gaff] SOURCE3 46 0.9817 1.1645
+angle h4 ca nb 51.800001 115.940002 ![gaff] SOURCE3 52 0.5536 0.7370
+angle ca ca nb 69.199996 122.629995 ![gaff] SOURCE3 83 0.9345 1.1249
+angle ca ca h4 48.199999 121.089992 ![gaff] SOURCE3 57 1.0923 1.4696
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca nb X 4.800000 2 180.000005 ![gaff] same as X-CA-NC-X
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+! type1 type2 type3 type4 k periodicity phi0
+impr ca h4 ca nb 1.100000 2 180.000005 ! Using default value
+impr ca ca ca ha 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nb 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in pure aromatic systems
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+67.177032 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PRM N1 nb -0.77559 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PRM C2 ca 0.79548 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 PRM H2 h5 -0.00575 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 PRM N3 nb -0.77559 14.00670 N 7 1.000000 0.000000 0
+4 MAIN 1 PRM C4 ca 0.53198 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 PRM H4 h4 0.05213 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 PRM C5 ca -0.59330 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 PRM H5 ha 0.18651 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 PRM C6 ca 0.53198 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 PRM H6 h4 0.05213 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.64552624 0.57360993 -1.04654562
+1 0.66634985 0.55381687 -0.91538334
+2 1.23450058 1.02450149 -1.69672861
+3 1.35485187 0.01758936 0.07306960
+4 0.65029370 -0.55922280 1.02997727
+5 1.20735669 -0.99837290 1.83898319
+6 -0.73092248 -0.60375413 1.00620491
+7 -1.29821066 -1.07372393 1.78636394
+8 -1.33764928 -0.00665871 -0.08267812
+9 -2.40864607 0.00672298 -0.18490035
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 8 1 2 1 3
+3 4 4 5 4 6 6 7
+6 8 8 9
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+8 0 1 0 1 2 0 1 3
+0 8 6 0 8 9 3 1 2
+1 3 4 3 4 5 3 4 6
+6 4 5 4 6 7 4 6 8
+8 6 7 6 8 9
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+8 0 1 2 8 0 1 3
+1 0 8 6 1 0 8 9
+0 1 3 4 2 1 3 4
+1 3 4 5 1 3 4 6
+3 4 6 7 3 4 6 8
+5 4 6 7 5 4 6 8
+4 6 8 0 4 6 8 9
+7 6 8 0 7 6 8 9
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+3 5 4 6 4 7 6 8
+0 2 1 3 0 6 8 9
+
+!:md_parameters
+log_file pyridine.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 8
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond ca nb 483.099991 1.342000 ![gaff] SOURCE3 104 0.0052 0.0076
+bond ca h5 347.200012 1.085000 ![gaff] SOURCE3 15 0.0038 0.0048
+bond ca h4 342.900008 1.088000 ![gaff] SOURCE3 57 0.0016 0.0026
+bond ca ca 478.399999 1.387000 ![gaff] SOURCE1 6228 0.0096 0.0147
+bond ca ha 344.299984 1.087000 ![gaff] SOURCE3 1496 0.0024 0.0045
+! type1 type2 type3 k a0
+angle ca nb ca 68.599997 115.860007 ![gaff] SOURCE3 46 0.9817 1.1645
+angle h5 ca nb 51.800001 116.350005 ![gaff] SOURCE3 30 0.4960 0.5545
+angle nb ca nb 71.199998 125.839993 ![gaff] SOURCE3 17 2.5680 4.1190
+angle ca ca nb 69.199996 122.629995 ![gaff] SOURCE3 83 0.9345 1.1249
+angle h4 ca nb 51.800001 115.940002 ![gaff] SOURCE3 52 0.5536 0.7370
+angle ca ca h4 48.199999 121.089992 ![gaff] SOURCE3 57 1.0923 1.4696
+angle ca ca ha 48.499999 120.010003 ![gaff] SOURCE3 2980 0.1509 0.2511
+angle ca ca ca 67.199999 119.970005 ![gaff] SOURCE3 1969 0.1024 0.3480
+! type1 type2 type3 type4 k periodicity phi0
+dihe X ca nb X 4.800000 2 180.000005 ![gaff] same as X-CA-NC-X
+dihe X ca ca X 3.620000 2 180.000005 ![gaff] intrpol.bsd.on C6H6
+! type1 type2 type3 type4 k periodicity phi0
+impr ca h4 ca nb 1.100000 2 180.000005 ! Using default value
+impr ca ca ca ha 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 nb ca nb 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nb 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in pure aromatic systems
+vdw ca 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 C in pure aromatic systems
+vdw h5 0.015000 1.359000 0.015000 1.359000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 2 electrwd. group
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+91.888016 0.979543 0.185413 -0.078218
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 PYR N1 na -0.20605 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 PYR H1 hn 0.32199 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 PYR C2 cc -0.20677 12.01070 C 6 1.000000 0.000000 0
+3 MAIN 1 PYR H2 h4 0.18440 1.00790 H 1 1.000000 0.000000 0
+4 MAIN 1 PYR C3 cd -0.19287 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 PYR H3 ha 0.15727 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 PYR C4 cd -0.19287 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 PYR H4 ha 0.15727 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 PYR C5 cc -0.20677 12.01070 C 6 1.000000 0.000000 0
+9 MAIN 1 PYR H5 h4 0.18440 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.71724422 0.64263389 -1.17255812
+1 -1.18466665 1.06226090 -1.94095259
+2 0.63409885 0.60134558 -1.00085910
+3 1.29598241 1.03943820 -1.71841878
+4 0.89319034 -0.05193064 0.16088435
+5 1.86343882 -0.24569281 0.57122558
+6 -0.36420112 -0.42550629 0.72175590
+7 -0.52761003 -0.95608174 1.63777609
+8 -1.32744439 0.01856387 -0.12589391
+9 -2.39347031 -0.05671111 -0.07270273
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 0 8 2 3
+2 4 4 5 6 7 6 8
+8 9 6 4
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+2 0 1 8 0 1 8 0 2
+0 2 3 0 2 4 0 8 6
+0 8 9 4 2 3 2 4 5
+8 6 7 6 8 9 7 6 4
+8 6 4 6 4 2 6 4 5
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 0 2 3 1 0 2 4
+8 0 2 3 8 0 2 4
+1 0 8 6 1 0 8 9
+2 0 8 6 2 0 8 9
+0 2 4 5 3 2 4 5
+7 6 8 0 7 6 8 9
+7 6 4 2 7 6 4 5
+8 6 4 2 8 6 4 5
+0 2 4 6 3 2 4 6
+4 6 8 0 4 6 8 9
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+1 2 0 8 0 3 2 4
+2 5 4 6 7 8 6 4
+0 6 8 9
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 8
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond hn na 406.600015 1.011000 ![gaff] SOURCE3 46 0.0076 0.0107
+bond cc na 438.799985 1.371000 ![gaff] SOURCE3 440 0.0107 0.0144
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cd ha 347.200012 1.085000 ![gaff] SOURCE3 740 0.0029 0.0039
+bond cd cd 418.299991 1.429000 ![gaff] SOURCE1 740 0.0058 0.0069
+! type1 type2 type3 k a0
+angle cc na hn 47.200002 124.660009 ![gaff] SOURCE3 38 4.3279 5.9689
+angle cc na cc 68.900001 109.900005 ![gaff] SOURCE3 109 1.2152 1.5547
+angle h4 cc na 50.200001 119.660010 ![gaff] SOURCE3 294 0.9445 2.4702
+angle cd cc na 72.900000 109.419999 ![gaff] SOURCE3 265 1.3410 2.6051
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cc cd ha 48.400002 122.889993 ![gaff] SOURCE3 584 2.3225 2.9334
+angle cd cd ha 46.599998 123.739996 ![gaff] SOURCE3 656 2.7165 3.3195
+angle cc cd cd 68.199995 114.190005 ![gaff] SOURCE3 517 5.4334 6.5960
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cc na X 1.700000 2 180.000005 ![gaff] statistic value from parm94
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe X cd cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw na 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N with three connected atoms
+vdw hn 0.015700 0.600000 0.015700 0.600000 1 1.008000 ![gaff] H bonded to nitrogen atoms
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 THZ N1 nc -0.46676 14.00670 N 7 1.000000 0.000000 0
+1 MAIN 1 THZ C2 cd 0.16265 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 THZ H2 h5 0.14281 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 THZ S3 ss -0.02110 32.06600 S 16 1.000000 0.000000 0
+4 MAIN 1 THZ C4 cd -0.25566 12.01070 C 6 1.000000 0.000000 0
+5 MAIN 1 THZ H4 h4 0.20267 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 THZ C5 cc 0.11790 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 THZ H5 h4 0.11749 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.68502284 0.66213288 -1.20429064
+1 0.58392558 0.64722099 -1.08479480
+2 1.25078217 1.08511488 -1.80164086
+3 1.19055953 -0.13623190 0.33022825
+4 -0.44050392 -0.46760066 0.78976746
+5 -0.68120535 -0.99248156 1.69013727
+6 -1.27720781 0.02600369 -0.13520720
+7 -2.34637574 -0.03897803 -0.10025209
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 6 1 2 1 3
+4 5 4 6 6 7 4 3
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+6 0 1 0 1 2 0 1 3
+0 6 4 0 6 7 3 1 2
+6 4 5 4 6 7 5 4 3
+6 4 3 4 3 1
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+6 0 1 2 6 0 1 3
+1 0 6 4 1 0 6 7
+5 4 6 0 5 4 6 7
+5 4 3 1 6 4 3 1
+0 1 3 4 2 1 3 4
+3 4 6 0 3 4 6 7
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+0 2 1 3 5 6 4 3
+0 4 6 7
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 22
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond cd nc 494.599991 1.335000 ![gaff] SOURCE3 203 0.0171 0.0239
+bond cc nc 431.599989 1.376000 ![gaff] SOURCE1 88 0.0000 0.0000
+bond cd h5 355.999995 1.079000 ![gaff] SOURCE3 40 0.0040 0.0051
+bond cd ss 279.299990 1.737000 ![gaff] SOURCE3 52 0.0162 0.0194
+bond cd h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+! type1 type2 type3 k a0
+angle cc nc cd 70.500001 107.470001 ![gaff] SOURCE3 26 4.9214 5.4053
+angle h5 cd nc 50.099999 125.379993 ![gaff] SOURCE3 40 1.6952 2.2157
+angle nc cd ss 66.500002 114.510000 ![gaff] SOURCE3 8 0.2795 0.3449
+angle cd cc nc 71.000000 114.980006 ![gaff] SOURCE3 23 4.6219 5.3935
+angle h4 cc nc 49.999998 120.030002 ![gaff] SOURCE3 16 1.9828 2.3863
+angle h5 cd ss 42.200002 122.000006 ![gaff] SOURCE3 6 0.5719 0.7237
+angle cc cd h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle h4 cd ss 43.000000 117.750002 ![gaff] SOURCE3 40 2.0527 3.1156
+angle cc cd ss 63.599996 118.170004 ![gaff] SOURCE3 37 3.1217 5.1653
+angle cd ss cd 67.000000 89.910001 ![gaff] SOURCE3 11 2.0978 2.2164
+angle na c2 os 73.885003 112.565001 ! Calculated with empirical approach
+angle h5 c2 os 51.700000 116.110006 ! same as hc-c2-os
+angle na c2 ss 83.420994 114.785004 ! Calculated with empirical approach
+angle h5 c2 ss 43.400001 115.620008 ! same as hc-c2-ss
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cd nc X 4.750000 2 180.000005 ![gaff] statistiv value from parm94
+dihe X cc nc X 4.750000 2 180.000005 ![gaff] statistic value from parm94
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe cd ss cd h4 1.100000 2 180.000005 ! same as X -c2-ss-X
+dihe cc cd ss cd 1.100000 2 180.000005 ! same as X -c2-ss-X
+dihe cd ss cd nc 1.100000 2 180.000005 ! same as X -c2-ss-X
+dihe cd ss cd h5 1.100000 2 180.000005 ! same as X -c2-ss-X
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na cc nd 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd nd 1.100000 2 180.000005 ! Using default value
+impr h5 na c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 na 1.100000 2 180.000005 ! Using default value
+impr c2 c2 na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na c2 ss 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 ss 1.100000 2 180.000005 ! Using default value
+impr h5 nc cd ss 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd ss 1.100000 2 180.000005 ! Using default value
+impr cd h4 cc nc 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw nc 0.170000 1.824000 0.170000 1.824000 7 14.010000 ![gaff] Sp2 N in non-pure aromatic systems
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw h5 0.015000 1.359000 0.015000 1.359000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 2 electrwd. group
+vdw ss 0.250000 2.000000 0.250000 2.000000 16 32.060001 ![gaff] Sp3 S in thio-ester and thio-ether
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
--- /dev/null
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 THN S1 ss 0.01628 32.06600 S 16 1.000000 0.000000 0
+1 MAIN 1 THN C2 cc -0.26225 12.01070 C 6 1.000000 0.000000 0
+2 MAIN 1 THN H2 h4 0.22253 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 THN C3 cd -0.10762 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 THN H3 ha 0.13920 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 THN C4 cd -0.10762 12.01070 C 6 1.000000 0.000000 0
+6 MAIN 1 THN H4 ha 0.13920 1.00790 H 1 1.000000 0.000000 0
+7 MAIN 1 THN C5 cc -0.26225 12.01070 C 6 1.000000 0.000000 0
+8 MAIN 1 THN H5 h4 0.22253 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z
+0 -0.89590541 0.81130865 -1.47777431
+1 0.75658207 0.61865763 -1.01919717
+2 1.53950967 1.00621227 -1.63855984
+3 0.87855165 -0.04288287 0.14567323
+4 1.82157289 -0.26712783 0.60708590
+5 -0.39245835 -0.41550229 0.70291345
+6 -0.50561883 -0.94938520 1.62738104
+7 -1.42617293 -0.02125586 -0.06222669
+8 -2.47100873 -0.16954277 0.11974439
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 7 1 2 1 3
+5 6 5 7 7 8 5 3
+3 4
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+7 0 1 0 1 2 0 1 3
+0 7 5 0 7 8 3 1 2
+7 5 6 5 7 8 6 5 3
+7 5 3 5 3 1 1 3 4
+5 3 4
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+7 0 1 2 7 0 1 3
+1 0 7 5 1 0 7 8
+6 5 7 0 6 5 7 8
+6 5 3 1 7 5 3 1
+0 1 3 5 2 1 3 5
+3 5 7 0 3 5 7 8
+0 1 3 4 2 1 3 4
+4 3 5 6 4 3 5 7
+
+!:impropers
+! a1 b1 c1 d1 a2 b2 c2 d2
+0 2 1 3 6 7 5 3
+0 5 7 8 1 5 3 4
+
+!:md_parameters
+log_file cyclopentadienyl.log
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 22
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond cc ss 279.299990 1.737000 ![gaff] SOURCE3 52 0.0162 0.0194
+bond cc h4 350.100004 1.083000 ![gaff] SOURCE3 599 0.0028 0.0037
+bond cc cd 504.000009 1.371000 ![gaff] SOURCE3 523 0.0156 0.0217
+bond cd ha 347.200012 1.085000 ![gaff] SOURCE3 740 0.0029 0.0039
+bond cd cd 418.299991 1.429000 ![gaff] SOURCE1 740 0.0058 0.0069
+! type1 type2 type3 k a0
+angle cc ss cc 67.000000 89.910001 ![gaff] SOURCE3 11 2.0978 2.2164
+angle h4 cc ss 43.000000 117.750002 ![gaff] SOURCE3 40 2.0527 3.1156
+angle cd cc ss 63.599996 118.170004 ![gaff] SOURCE3 37 3.1217 5.1653
+angle cd cc h4 47.200002 129.110000 ![gaff] SOURCE3 418 2.0265 3.1355
+angle cc cd ha 48.400002 122.889993 ![gaff] SOURCE3 584 2.3225 2.9334
+angle cd cd ha 46.599998 123.739996 ![gaff] SOURCE3 656 2.7165 3.3195
+angle cc cd cd 68.199995 114.190005 ![gaff] SOURCE3 517 5.4334 6.5960
+angle na c2 os 73.885003 112.565001 ! Calculated with empirical approach
+angle h5 c2 os 51.700000 116.110006 ! same as hc-c2-os
+! type1 type2 type3 type4 k periodicity phi0
+dihe X cc cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe X cd cd X 4.000000 2 180.000005 ![gaff] statistic value of parm94
+dihe cc os cc h4 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cc os cc cd 1.050000 2 180.000005 ! same as X -c2-os-X
+dihe cc ss cc h4 1.100000 2 180.000005 ! same as X -c2-ss-X
+dihe cc ss cc cd 1.100000 2 180.000005 ! same as X -c2-ss-X
+! type1 type2 type3 type4 k periodicity phi0
+impr cd h4 cc na 1.100000 2 180.000005 ! Using default value
+impr cc cd cd ha 1.100000 2 180.000005 ! Using default value
+impr cc cc na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr h5 na cc nd 1.100000 2 180.000005 ! Using default value
+impr cc h4 cd nd 1.100000 2 180.000005 ! Using default value
+impr h5 na c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 os 1.100000 2 180.000005 ! Using default value
+impr c2 h4 c2 na 1.100000 2 180.000005 ! Using default value
+impr c2 c2 na hn 1.100000 2 180.000005 ! General improper torsional angle (2 general atom types)
+impr cd h4 cc os 1.100000 2 180.000005 ! Using default value
+impr cd h4 cc ss 1.100000 2 180.000005 ! Using default value
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw ss 0.250000 2.000000 0.250000 2.000000 16 32.060001 ![gaff] Sp3 S in thio-ester and thio-ether
+vdw cc 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems
+vdw h4 0.015000 1.409000 0.015000 1.409000 1 1.008000 ![gaff] H bonded to non-sp3 carbon with 1 electrwd. group
+vdw cd 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp2 carbons in non-pure aromatic systems, identical to cc
+vdw ha 0.015000 1.459000 0.015000 1.459000 1 1.008000 ![gaff] H bonded to aromatic carbon
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.000000
+0.000000 0.000000 0.000000
+43.636372 1.000000 0.000000 0.000000
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+
}
# Create resp input by respgen
- if !call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input1 -f resp1", "respgen (stage 1)") \
- || !call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input2 -f resp2", "respgen (stage 2)")
- error_message_box("Cannot run respgen.")
+ status = call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input1 -f resp1", "respgen (stage 1)")
+ if status == 0
+ status = call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input2 -f resp2", "respgen (stage 2)")
+ end
+ if status != 0
+ error_message_box("Cannot run respgen: status = #{status}")
Dir.chdir(cwd)
return
end
}
# Run resp
- if !call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input1 -o resp.output1 -e resp.esp -t qout_stage1", "resp (stage 1)") \
- || !call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input2 -o resp.output2 -e resp.esp -q qout_stage1 -t qout_stage2", "resp (stage 2)")
- error_message_box("Cannot run resp.")
+ status = call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input1 -o resp.output1 -e resp.esp -t qout_stage1", "resp (stage 1)")
+ if status == 0
+ status = call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input2 -o resp.output2 -e resp.esp -q qout_stage1 -t qout_stage2", "resp (stage 2)")
+ if status == 255 && File.exist?("punch")
+ status = 0 # Ignore error at the second stage
+ end
+ end
+ if status != 0
+ error_message_box("Cannot run resp: status = #{status}")
Dir.chdir(cwd)
return
end
parameterFrame = NULL;
parameterFilesFrame = NULL;
consoleFrame = NULL;
+ m_CountNamedFragments = 0;
+ m_NamedFragments = (char **)(-1); /* Will be set to NULL after Ruby interpreter is initialized */
}
bool MyApp::OnInit(void)
wxSetWorkingDirectory(cwd);
MyAppCallback_showScriptMessage("%% ");
+
+ /* Build the predefined fragments menu */
+ m_NamedFragments = NULL;
+ UpdatePredefinedFragmentMenu(GetMainFrame()->GetMenuBar());
+ UpdatePredefinedFragmentMenu(consoleFrame->GetMenuBar());
+
}
/* Open given files as MyDocument */
m_docManager->FileHistoryAddFilesToMenu(*out_file_history_menu);
m_docManager->FileHistoryUseMenu(*out_file_history_menu); // Should be removed when menu is discarded
}
-
+ /* Build "Open Predefined" */
+ wxMenu *predefined_menu = new wxMenu;
+ file_menu->Append(myMenuID_PredefinedFragment, _T("Open Predefined"), predefined_menu);
+
file_menu->AppendSeparator();
file_menu->Append(wxID_CLOSE, _T("&Close\tCtrl-W"));
file_menu->Append(wxID_SAVE, _T("&Save\tCtrl-S"));
menu_bar->Append(help_menu, _T("&Help"));
UpdateScriptMenu(menu_bar);
+ if (m_NamedFragments != (char **)(-1))
+ UpdatePredefinedFragmentMenu(menu_bar);
return menu_bar;
}
}
void
+MyApp::UpdatePredefinedFragmentMenu(wxMenuBar *mbar)
+{
+ int i, n;
+ wxMenuItem *fmenuItem = mbar->FindItem(myMenuID_PredefinedFragment);
+ wxMenu *fmenu = (fmenuItem != NULL ? fmenuItem->GetSubMenu() : NULL);
+ if (fmenu == NULL)
+ return;
+ if (m_NamedFragments == (char **)(-1))
+ return;
+
+ /* Rebuild sNamedFragments array */
+ if (m_NamedFragments != NULL) {
+ for (i = 0; i < m_CountNamedFragments; i++) {
+ free(m_NamedFragments[i * 2]);
+ free(m_NamedFragments[i * 2 + 1]);
+ }
+ free(m_NamedFragments);
+ }
+ m_NamedFragments = NULL;
+ m_CountNamedFragments = 0;
+ if (MolActionCreateAndPerform(NULL, SCRIPT_ACTION(";i"), "proc { $named_fragments.length }", &n) != 0 || n <= 0)
+ return;
+ m_CountNamedFragments = n;
+ m_NamedFragments = (char **)calloc(sizeof(char *), n * 2);
+ for (i = 0; i < n; i++) {
+ if (MolActionCreateAndPerform(NULL, SCRIPT_ACTION("i;s"), "proc { |i| $named_fragments[i][0] }", i, &m_NamedFragments[i * 2]) != 0 ||
+ MolActionCreateAndPerform(NULL, SCRIPT_ACTION("i;s"), "proc { |i| $named_fragments[i][1] }", i, &m_NamedFragments[i * 2 + 1]) != 0)
+ break;
+ }
+ if (i < n) {
+ for (i = 0; i < m_CountNamedFragments; i++) {
+ if (m_NamedFragments[i * 2] != NULL)
+ free(m_NamedFragments[i * 2]);
+ if (m_NamedFragments[i * 2 + 1] != NULL)
+ free(m_NamedFragments[i * 2 + 1]);
+ }
+ free(m_NamedFragments);
+ m_CountNamedFragments = 0;
+ m_NamedFragments = NULL;
+ return;
+ }
+
+ wxMenu *predefined_submenu = NULL;
+ wxString stitle;
+ int sn;
+ for (i = sn = 0; i < m_CountNamedFragments; i++) {
+ if (strcmp(m_NamedFragments[i * 2 + 1], "-") == 0) {
+ if (predefined_submenu != NULL) {
+ fmenu->Append(myMenuID_PredefinedFragment + 1 + sn, stitle, predefined_submenu);
+ }
+ predefined_submenu = new wxMenu;
+ stitle = wxString(m_NamedFragments[i * 2], WX_DEFAULT_CONV);
+ sn = i;
+ } else {
+ wxString mtitle(m_NamedFragments[i * 2], WX_DEFAULT_CONV);
+ (predefined_submenu != NULL ? predefined_submenu : fmenu)->Append(myMenuID_PredefinedFragment + 1 + i, mtitle);
+ }
+ }
+ if (predefined_submenu != NULL)
+ fmenu->Append(myMenuID_PredefinedFragment + 1 + sn, stitle, predefined_submenu);
+ Connect(myMenuID_PredefinedFragment + 1, myMenuID_PredefinedFragment + m_CountNamedFragments, wxEVT_COMMAND_MENU_SELECTED, wxCommandEventHandler(MyApp::OnFragmentMenuSelected), NULL, this);
+}
+
+void
+MyApp::OnFragmentMenuSelected(wxCommandEvent& event)
+{
+ int index = event.GetId() - myMenuID_PredefinedFragment - 1;
+ if (index < 0 || index >= m_CountNamedFragments)
+ return;
+ // Open a predefined fragment as a new file
+ char errbuf[1024];
+ Molecule *mol = MoleculeNew();
+ char *fullname;
+ asprintf(&fullname, "%s/Scripts/mbsf/%s", (const char *)(FindResourcePath().mb_str(wxConvFile)), m_NamedFragments[index * 2 + 1]);
+ if (MoleculeLoadMbsfFile(mol, fullname, errbuf, sizeof(errbuf)) != 0) {
+ MyAppCallback_errorMessageBox("Cannot open named fragment %s: %s", m_NamedFragments[index * 2], errbuf);
+ free(fullname);
+ return;
+ }
+ free(fullname);
+ MyDocument *doc = (MyDocument *)(DocManager()->CreateDocument(wxT(""), wxDOC_NEW));
+ wxString title(m_NamedFragments[index * 2], WX_DEFAULT_CONV);
+ title = _T("*") + title + _T("*");
+ doc->SetMolecule(mol);
+ if (mol->natoms > 1000)
+ mol->mview->lineMode = 1;
+ MainView_resizeToFit(mol->mview);
+
+ // Change the window title
+ doc->SetTitle(title);
+ // Propagate the change of the window title
+ wxList::compatibility_iterator node = doc->GetViews().GetFirst();
+ while (node) {
+ wxView *view = (wxView *)node->GetData();
+ view->OnChangeFilename();
+ node = node->GetNext();
+ }
+}
+
+void
MyApp::OnUpdateUI(wxUpdateUIEvent& event)
{
int uid = event.GetId();
else if (methodType == 2) /* Class method (with molecule as an only argument) */
event.Enable(true);
}
+ } else if (uid >= myMenuID_PredefinedFragment && uid <= myMenuID_PredefinedFragment + m_CountNamedFragments) {
+ event.Enable(true);
} else {
switch (uid) {
case myMenuID_ExecuteScript:
default:
if (mview == NULL)
event.Enable(false);
- else event.Skip();
+ else
+ event.Skip();
}
}
}
m_processExitCode = 0;
long pid = ::wxExecute(cmdstr, flag, proc);
if (pid == 0) {
- MyAppCallback_errorMessageBox("Cannot start %s", procname);
+ // MyAppCallback_errorMessageBox("Cannot start %s", procname);
proc->Detach();
HideProgressPanel();
#if LOG_SUBPROCESS
if (m_processTerminated || !wxProcess::Exists(pid)) {
if (m_processExitCode != 0) {
/* Error from subprocess */
- MyAppCallback_errorMessageBox("%s failed with exit code %d.", procname, m_processExitCode);
- status = m_processExitCode;
+ // MyAppCallback_errorMessageBox("%s failed with exit code %d.", procname, m_processExitCode);
+ status = (m_processExitCode & 255);
} else status = 0;
break;
}
::wxKill(pid, wxSIGTERM, &rc, kflag) != 0
#endif
) {
- const char *emsg;
switch (rc) {
- case wxKILL_BAD_SIGNAL: emsg = "no such signal"; break;
- case wxKILL_ACCESS_DENIED: emsg = "permission denied"; break;
- case wxKILL_NO_PROCESS: emsg = "no such process"; break;
- default: emsg = "unknown error"; break;
+ case wxKILL_BAD_SIGNAL: status = -3; break; /* No such signal */
+ case wxKILL_ACCESS_DENIED: status = -4; break; /* Permission denied */
+ case wxKILL_NO_PROCESS: status = -5; break; /* No such process */
+ default: status = -6; break; /* unknown error */
}
- MyAppCallback_errorMessageBox("Cannot kill subprocess: %s", emsg);
- }
+ } else status = -2; /* User interrupt */
proc->Detach();
- status = -2;
break;
}
while (in->CanRead()) {
myMenuID_ExecuteScript = 300,
myMenuID_OpenConsoleWindow = 301,
myMenuID_CustomScript = 302,
+ myMenuID_PredefinedFragment = 350,
myMenuID_MyLastMenuItem = 499
};
void UpdateScriptMenu(wxMenuBar *mbar);
void OnScriptMenuModified(wxCommandEvent& event);
void OnScriptMenuSelected(wxCommandEvent& event);
+ void UpdatePredefinedFragmentMenu(wxMenuBar *mbar);
+ void OnFragmentMenuSelected(wxCommandEvent& event);
+
void OnUpdateUI(wxUpdateUIEvent &event);
void OnExecuteScript(wxCommandEvent &event);
void OnOpenConsoleWindow(wxCommandEvent &event);
char **scriptMenuCommands;
char **scriptMenuTitles;
bool scriptMenuModifiedEventPosted;
+
+ int m_CountNamedFragments;
+ char **m_NamedFragments;
#if __WXMSW__
wxSingleInstanceChecker *m_checker;
asprintf(&p, "\"%s/antechamber\" -i mol.pdb -fi pdb -o mol.ac -fo ac %s", ante_dir, buf);
status = MyAppCallback_callSubProcess(p, "antechamber");
- if (status == 0) {
+ if (status != 0) {
+ MyAppCallback_errorMessageBox("Antechamber failed: status = %d.", status);
+ } else {
asprintf(&p, "\"%s/parmchk\" -i mol.ac -f ac -o frcmod", ante_dir);
status = MyAppCallback_callSubProcess(p, "parmchk");
+ if (status != 0)
+ MyAppCallback_errorMessageBox("Parmchk failed: status = %d.", status);
}
}
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