From 5fefacf6913d69246115cb265db3e4eb7cf3e726 Mon Sep 17 00:00:00 2001 From: toshinagata1964 Date: Sun, 20 Oct 2013 06:30:56 +0000 Subject: [PATCH] The built-in structures of cycloalkanes are updated git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@404 a2be9bc6-48de-4e38-9406-05402d4bc13c --- Scripts/mbsf/alicyclic/cyclobutane.mbsf | 75 +++++++++++------------ Scripts/mbsf/alicyclic/cyclohexane.mbsf | 101 ++++++++++++++++--------------- Scripts/mbsf/alicyclic/cyclopentane.mbsf | 69 ++++++++++----------- Scripts/mbsf/alicyclic/cyclopropane.mbsf | 60 +++++++++--------- Scripts/mbsf/fragment_def.rb | 2 + 5 files changed, 155 insertions(+), 152 deletions(-) diff --git a/Scripts/mbsf/alicyclic/cyclobutane.mbsf b/Scripts/mbsf/alicyclic/cyclobutane.mbsf index 71fe739..3c7738b36 100644 --- a/Scripts/mbsf/alicyclic/cyclobutane.mbsf +++ b/Scripts/mbsf/alicyclic/cyclobutane.mbsf @@ -1,32 +1,32 @@ !: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 +0 MAIN 1 CBT C1 cy -0.03368 12.01070 C 6 1.000000 0.000000 0 +1 MAIN 1 CBT H11 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +2 MAIN 1 CBT H12 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +3 MAIN 1 CBT C2 cy -0.03368 12.01070 C 6 1.000000 0.000000 0 +4 MAIN 1 CBT H21 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +5 MAIN 1 CBT H22 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +6 MAIN 1 CBT C3 cy -0.03368 12.01070 C 6 1.000000 0.000000 0 +7 MAIN 1 CBT H31 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +8 MAIN 1 CBT H32 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +9 MAIN 1 CBT C4 cy -0.03368 12.01070 C 6 1.000000 0.000000 0 +10 MAIN 1 CBT H41 hc 0.01684 1.00790 H 1 1.000000 0.000000 0 +11 MAIN 1 CBT H42 hc 0.01684 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 +! idx x y z [sx sy sz] +0 0.32008000 0.77648000 0.24985200 +1 0.36988500 1.46428700 -0.58774200 +2 -0.71327800 0.48035900 0.39029800 +3 1.37846800 -0.34339500 0.13275100 +4 1.72400100 -0.60820200 -0.86008800 +5 1.06168500 -1.24892600 0.63948900 +6 2.31811400 0.50687700 1.01712600 +7 2.99356800 1.11026200 0.41979000 +8 2.89664400 -0.00674200 1.77656100 +9 1.08563900 1.31682000 1.47866000 +10 1.19493600 2.39136900 1.57161900 +11 0.67716200 0.93115600 2.40684700 !:bonds ! from1 to1 from2 to2 from3 to3 from4 to4 @@ -76,11 +76,12 @@ debug_output_level 0 step 0 coord_output_freq 10 energy_output_freq 10 -coord_frame 135 +coord_frame 336 timestep 1 cutoff 9 electro_cutoff 9 pairlist_distance 10 +switch_distance 8 temperature 300 andersen_freq 50 andersen_coupling 0.1 @@ -101,18 +102,16 @@ 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 +bond cy hc 334.500013 1.094000 ![gaff] SOURCE3 63 0.0012 0.0014 +bond cy cy 286.799986 1.554000 ![gaff] SOURCE1 742 0.0013 0.0041 ! 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 +angle hc cy hc 39.199999 109.040002 ![gaff] SOURCE3 28 0.4802 0.5962 +angle cy cy hc 44.799999 115.139996 ![gaff] SOURCE3 114 0.7232 0.8364 +angle cy cy cy 70.199997 87.610003 ![gaff] SOURCE3 32 1.1419 1.5407 ! 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 +dihe X cy cy X 0.160000 3 0.000000 ![gaff] same as X-c3-c3-X ! 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 cy 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp3 carbons in square systems vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group !:velocity @@ -147,9 +146,9 @@ vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to alipha !: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 +0.702022 +-0.114659 -0.035178 -0.097297 +131.498245 -0.517758 -0.305212 -0.799232 !:view show_unit_cell 0 diff --git a/Scripts/mbsf/alicyclic/cyclohexane.mbsf b/Scripts/mbsf/alicyclic/cyclohexane.mbsf index 967290d..8ccbf56 100644 --- a/Scripts/mbsf/alicyclic/cyclohexane.mbsf +++ b/Scripts/mbsf/alicyclic/cyclohexane.mbsf @@ -16,82 +16,82 @@ 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 +16 MAIN 1 CHX H62 hc -0.01014 1.00790 H 1 1.000000 0.000000 0 +17 MAIN 1 CHX H61 hc -0.01014 1.00790 H 1 1.000000 0.000000 0 !:positions ; frame 0 -! idx x y z +! idx x y z [sx sy sz] 0 -0.37191979 -0.01470847 -0.04533071 -1 -0.75956029 -0.01758412 -1.06061947 -2 -0.69639261 -0.94754613 0.41364630 +1 -0.69639261 -0.94754613 0.41364630 +2 -0.75956029 -0.01758412 -1.06061947 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 +7 1.51218359 -0.82462353 1.87714401 +8 2.81961168 0.18159574 1.31107702 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 +13 -0.70516396 0.36153957 2.72037649 +14 -0.77379399 2.10387643 2.67759924 15 -0.95755584 1.16339033 0.73952318 -16 -2.04069583 1.08442098 0.78021752 -17 -0.73327535 2.09064904 0.21414856 +16 -0.73327535 2.09064904 0.21414856 +17 -2.04069583 1.08442098 0.78021752 !: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 2 0 1 3 4 3 5 +6 7 6 8 3 6 9 10 +9 11 6 9 12 13 12 14 +9 12 15 17 15 16 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 +2 0 1 4 3 5 7 6 8 +4 3 6 5 3 6 3 6 7 +3 6 8 10 9 11 7 6 9 +8 6 9 3 6 9 6 9 10 +6 9 11 13 12 14 10 9 12 +11 9 12 6 9 12 9 12 13 +9 12 14 17 15 16 13 12 15 +14 12 15 9 12 15 12 15 17 +12 15 16 2 0 3 1 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 +2 0 15 1 0 15 3 0 15 +0 15 17 0 15 16 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 +4 3 6 7 4 3 6 8 +5 3 6 7 5 3 6 8 7 6 9 10 7 6 9 11 +8 6 9 10 8 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 +10 9 12 13 10 9 12 14 +11 9 12 13 11 9 12 14 +6 9 12 13 6 9 12 14 +13 12 15 17 13 12 15 16 +14 12 15 17 14 12 15 16 +9 12 15 17 9 12 15 16 +2 0 3 4 2 0 3 5 +2 0 3 6 1 0 3 4 +1 0 3 5 1 0 3 6 +2 0 15 17 2 0 15 16 +2 0 15 12 1 0 15 17 +1 0 15 16 1 0 15 12 +3 0 15 17 3 0 15 16 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 +0 3 6 7 0 3 6 8 +0 3 6 9 7 6 9 12 +8 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 +6 9 12 15 13 12 15 0 +14 12 15 0 9 12 15 0 !:md_parameters log_file (null) @@ -108,6 +108,7 @@ timestep 1 cutoff 9 electro_cutoff 9 pairlist_distance 10 +switch_distance 8 temperature 300 andersen_freq 50 andersen_coupling 0.1 @@ -186,9 +187,9 @@ vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to alipha !: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 +0.595067 +-0.038946 -0.063301 -0.104564 +123.340775 0.160038 -0.958649 0.235331 !:view show_unit_cell 0 diff --git a/Scripts/mbsf/alicyclic/cyclopentane.mbsf b/Scripts/mbsf/alicyclic/cyclopentane.mbsf index 91d3fa7..8bcd050 100644 --- a/Scripts/mbsf/alicyclic/cyclopentane.mbsf +++ b/Scripts/mbsf/alicyclic/cyclopentane.mbsf @@ -1,38 +1,38 @@ !: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 +0 MAIN 1 CPN C1 c3 0.01466 12.01070 C 6 1.000000 0.000000 0 +1 MAIN 1 CPN H11 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +2 MAIN 1 CPN H12 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +3 MAIN 1 CPN C2 c3 0.01466 12.01070 C 6 1.000000 0.000000 0 +4 MAIN 1 CPN H21 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +5 MAIN 1 CPN H22 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +6 MAIN 1 CPN C3 c3 0.01466 12.01070 C 6 1.000000 0.000000 0 +7 MAIN 1 CPN H31 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +8 MAIN 1 CPN H32 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +9 MAIN 1 CPN C4 c3 0.01466 12.01070 C 6 1.000000 0.000000 0 +10 MAIN 1 CPN H41 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +11 MAIN 1 CPN H42 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +12 MAIN 1 CPN C5 c3 0.01466 12.01070 C 6 1.000000 0.000000 0 +13 MAIN 1 CPN H51 hc -0.00733 1.00790 H 1 1.000000 0.000000 0 +14 MAIN 1 CPN H52 hc -0.00733 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 +! idx x y z [sx sy sz] +0 -0.33442540 0.21615778 0.45111071 +1 -0.47373300 1.01704520 -0.27177307 +2 -1.12407878 -0.50981202 0.28708980 +3 1.07041764 -0.38714499 0.31035494 +4 1.38446551 -0.47922541 -0.72376218 +5 1.07764186 -1.38788045 0.73286621 +6 1.99782424 0.54288154 1.13256757 +7 2.62952920 1.14208574 0.48568788 +8 2.66271866 -0.03603847 1.76448163 +9 1.06098796 1.44377978 1.97625939 +10 1.02751155 2.44420304 1.55427825 +11 1.39553886 1.54570099 3.00299701 +12 -0.32731208 0.79714180 1.86727435 +13 -1.13516122 1.49833047 2.04948641 +14 -0.42523609 -0.00743241 2.59284831 !:bonds ! from1 to1 from2 to2 from3 to3 from4 to4 @@ -95,6 +95,7 @@ timestep 1 cutoff 9 electro_cutoff 9 pairlist_distance 10 +switch_distance 8 temperature 300 andersen_freq 50 andersen_coupling 0.1 @@ -167,9 +168,9 @@ vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to alipha !: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 +0.636059 +-0.080057 -0.045731 -0.120222 +90.213722 0.560648 0.788788 -0.251968 !:view show_unit_cell 0 diff --git a/Scripts/mbsf/alicyclic/cyclopropane.mbsf b/Scripts/mbsf/alicyclic/cyclopropane.mbsf index 511decc..e8dd78d 100644 --- a/Scripts/mbsf/alicyclic/cyclopropane.mbsf +++ b/Scripts/mbsf/alicyclic/cyclopropane.mbsf @@ -1,26 +1,26 @@ !: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 +0 MAIN 1 CPP C1 cx -0.25082 12.01070 C 6 1.000000 0.000000 0 +1 MAIN 1 CPP H11 hc 0.12541 1.00790 H 1 1.000000 0.000000 0 +2 MAIN 1 CPP H12 hc 0.12541 1.00790 H 1 1.000000 0.000000 0 +3 MAIN 1 CPP C2 cx -0.25082 12.01070 C 6 1.000000 0.000000 0 +4 MAIN 1 CPP H21 hc 0.12541 1.00790 H 1 1.000000 0.000000 0 +5 MAIN 1 CPP H22 hc 0.12541 1.00790 H 1 1.000000 0.000000 0 +6 MAIN 1 CPP C3 cx -0.25082 12.01070 C 6 1.000000 0.000000 0 +7 MAIN 1 CPP H31 hc 0.12541 1.00790 H 1 1.000000 0.000000 0 +8 MAIN 1 CPP H32 hc 0.12541 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 +! idx x y z [sx sy sz] +0 0.43392657 0.34677819 0.72704995 +1 0.13994072 1.18797449 0.12421963 +2 -0.31839425 0.02404579 1.42511890 +3 1.31396152 -0.69359437 0.10627000 +4 1.61627799 -0.55735546 -0.91719794 +5 1.15795080 -1.72127604 0.38371236 +6 1.87011191 0.23942341 1.13698741 +7 2.54927132 1.00787803 0.81192845 +8 2.09095342 -0.15605291 2.11283096 !:bonds ! from1 to1 from2 to2 from3 to3 from4 to4 @@ -67,6 +67,7 @@ timestep 1 cutoff 9 electro_cutoff 9 pairlist_distance 10 +switch_distance 8 temperature 300 andersen_freq 50 andersen_coupling 0.1 @@ -87,17 +88,16 @@ 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 +bond cx hc 345.800001 1.086000 ![gaff] SOURCE3 44 0.0009 0.0011 +bond cx cx 337.299999 1.499000 ![gaff] SOURCE1 1204 0.0159 0.0183 ! 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 +angle hc cx hc 38.600000 114.470002 ![gaff] SOURCE3 19 0.2816 0.3295 +angle cx cx hc 45.800000 117.919992 ![gaff] SOURCE3 92 0.7174 1.1927 +angle cx cx cx 85.300004 63.750001 ![gaff] SOURCE2 11 6.2810 11.0052 ! 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 X cx cx X 0.160000 3 0.000000 ![gaff] same as X-c3-c3-X ! 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 cx 0.086000 1.908000 0.086000 1.908000 6 12.010000 ![gaff] Sp3 carbons in triangle systems vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group !:velocity @@ -126,9 +126,9 @@ vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to alipha !: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 +0.757698 +-0.120611 0.003582 -0.065683 +97.036163 -0.929609 0.218390 -0.296873 !:view show_unit_cell 0 diff --git a/Scripts/mbsf/fragment_def.rb b/Scripts/mbsf/fragment_def.rb index 44136b6..caeccc2 100644 --- a/Scripts/mbsf/fragment_def.rb +++ b/Scripts/mbsf/fragment_def.rb @@ -38,6 +38,8 @@ class Molecule ["cyclooctyl", "cyclooctane", "H11"], ["C8H15", "cyclooctyl"], + ["cyclohexane (twist boat)", "alicyclic/cyclohexane-twist-boat.mbsf"], + "Aromatic", ["benzene", "aromatic/benzene.mbsf"], ["C6H6", "benzene"], -- 2.11.0