Step Four: Energy Minimization by Molecular Mechanics

Step Four: Ring Fusion

1. Ring fusion by double-click and type-in

+Molby has a capability to create a fused ring structure. As an example, here is presented yet another method to make indane. This time, we start from a benzene. +

+Choose "select" mode, and select C1 and C2 by clicking on the C1-C2 bond. +

+Double-click on the selection, and enter "cyclopentane" in the dialog box. +

+After pressing "OK", you will see a five-membered ring fused to the benzene ring. +

+Ring fusion also works when three or more atoms are selected in the original structure. For example, select the consecutive three carbons in indane as follows. +

+Double-click on the selection, and enter "C6H6" (or "benzene"). +

+Now we have acenaphthene...almost. +

+As shown in the above figure, there is an extra, leftover hydrogen atom on one bridgehead carbon. After all, Molby is not so smart --- it just removes one hydrogen from each terminal carbon atoms in the selection, and connect a portion of the fusing fragment ("benzene" in this case) so that the newly created ring has the same number of atoms. Consequently, the stereochemistry may become strange when sp3 carbons are present either in the original structure or in the fusing fragment. You may need to remove/append hydrogen atoms and clean up structures (see "Energy Minimization" for detail). +

2. Ring fusion by copy-and-paste

+There is another way to make a ring fused structure, which includes copy and paste. Starting again from a benzene. +

+Open the "File" menu, and select "Open Predefined" → "Alicyclic" → "cyclopentane". +

+A new window named "*cyclopentane*" opens with one cyclopentane molecule. Select a portion containing three CH2 groups, and copy it by command-C or ctrl-C. +

+Return to the benzene molecule again, and this time select H1 and H2 (not C1 and C2). +

+Do paste by command-V or ctrl-V. You now get a indane molecule. +

+This "copy-and-paste" actually works in a similar way to previously described example (see "Cut/Copy/Paste"). When both the current selection and the fragment in the pasteboard have two terminals, they are connected and ring fusion takes place. This method of ring fusion is slightly more complicated than the "double-click and type-in" method, but it may be easier to understand. +

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+é¸æé¨åãããã«ã¯ãªãã¯ãã¦ããã¤ã¢ãã°ããã¯ã¹ã« "cyclopentane" ã¨å¥åãã¾ãã +

+"OK" ãæ¼ãã¨ãï¼å¡ç°ããã³ã¼ã³ç°ã«ç¸®ç°ãã¾ãã +

+é¸æé¨åãããã«ã¯ãªãã¯ãã¦ã"C6H6"ï¼ã¾ãã¯ "benzene"ï¼ã¨å¥åãã¾ãã +

+ããããã¨ãã¢ã»ãããã³ãã§ãã¾ã...ã ãããã +

2. ã³ãã¼ï¼ãã¼ã¹ãã«ããç¸®ç°

+"File" ã¡ãã¥ã¼ãéãã"Open Predefined" → "Alicyclic" → "cyclopentane" ãé¸ãã§ãã ããã +

+ +

+ + + +

Step Five: Edit a Molecule: Using a Property Table

1. The Property Table of a Molecule

+A molecule has many properties. It has a set of atoms and bonds. An atom has a name, an atom type, an element, a weight (which can be derived from the element), a charge, coordinates, and so on. According to the custom in the biomolecular modeling, atoms are grouped in "residues." It also has a set of parameters used in molecular mechanics. Molby also has a limited support for quantum chemical calculations. In relation to that, a molecule in Molby can retain extra information such as MO coefficients. +

+Many of these information are accessible via the property table. The table is on the left side of the model window. +

+The table now shows the properties of each atom, namely its name, type, element, "residue" name and index, coordinates and partial charge. The property can be edited by double-clicking on the text. +

+When return (enter) or tab key is pressed, the edited value is finalized, and editing will continue on another cell. Pressing return, shift-return, tab, or shift-tab should cause editing of the bottom, above, right, or left cell, respectively. If you want to finish editing, use option- (or alt-) return key combination. +

+Several points are worth mentioning here. +

+(1) The atom index (the leftmost column) cannot be edited. If you want to change the order of the atoms, try using a "drag-and-drop" feature, as shown in the figure below. +

+(2) The residue column shows the residue name and index separated by a period. Manual editing of this cell may lead to a surprising result. For example, if you change the residue name of atom 0 from "RES" to "XXX", all atoms having residue index "1" will also have the new residue name "XXX". +

+This behavior is based on the principle that all residue names and indices should be consistent, i.e. the atoms having the same residue index should have the same residue name. This is sometimes convenient, but in many cases it causes confusion. +

+A more recommended way to change the residue name and index is to use the menu command "Assign Residue...", in the "Script" menu, after selecting atoms you want to assign one residue name and index. +

+ + + +

+ +

2. The Bond/Angle/Dihedral/Improper Table

+The property table can also show other information. The type of information can be selected at the popup menu. +

+The bond, angle, dihedral, and improper tables show the indices, names, and types of the constituent atoms. In addition, the quantities (bond lengths, angles, etc.) and the molecular mechanics parameters (only after MM/MD calculation is performed) are also shown. +

+The bonds, angles, etc. are not editable in the property table. At present, the only way to create/delete bonds from GUI is to use the mouse operation "Bond" or "Erase". +

+ +

3. The Parameter Table

+The parameter table shows the molecular mechanics parameters in one table. +

+The parameters are grouped in several classes, namely "VDWs", "Bonds", "Angles", "Dihedrals", "Impropers", and "VDW Pairs". +

+The "VDWs" parameters are for the van der Waals nonbonding interaction, described by "eps" (the energy at the potential minimum in kcal/mol), "r" (the van der Waals radius in Å, which is half of the interatomic distance at the equilibrium state), "eps14", "r14" (eps and r for the pair of atoms separated by exactly three bonds. In many applications, the same parameters with the ordinary pair are used with a specific factor multiplied), "atomNo" (the atomic number), "weight" (the atomic weight). The last two are usually overridden by the atom parameters. +

+The "Bonds" parameters consist of "k" (the force constant in kcal/mol/Å²) and "r0" (the equilibrium bond length). The "Angles" parameters consist of "k" (the force constant in kcal/mol/radian²) and "a0" (the equilibrium bond angle). The "Dihedrals" and "Impropers" parameters consist of "k" (the force constant in kcal/mol/radian²), "period" (the periodicity), and "phi0" (the equilibrium torsion angle in degree). The "VDW Pairs" parameters are (rarely) used to describe pair-specific van der Waals interactions, and consist of "eps", "r", "eps14", and "r14". +

+There is another important property for each parameter, that is, whether the parameter is taken from the "global" source (i.e. not specific to this molecule), or it is "local" (specific to this molecule), or "undefined". This property is shown by the color of the row. The global parameters are shown in white cells, the local ones in pale yellow, and the undefined ones in red. +

+You can edit the parameters (although you need to be familiar with MM parameters and to know what you are doing!), but only if they are "local" or "undefined" parameters. The "global" parameters cannot be edited because it may be also used in other molecules, where the edited parameters may not be appropriate. If you want to modify some parameters but they are "global", then you can make them "local" by copying the parameters and the pasting. +

+Another way to create a "local" parameter is to use the "Create New Parameter" menu command in the Edit menu. You can choose the parameter type in the submenu. +

+If some parameters are not to be used for calculation, you can "cut" the parameters from the table. This feature is useful when you have many duplicated parameters having different force constants. (In actual calculation, the parameter appearing later in the table will be used.) +

+ +

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+æ®åºåã¨æ®åºçªå·ãå¤æ´ãããå§ãã®æ¹æ³ã¯ãå¤æ´ãããååãé¸æãã¦ "Script" ã¡ãã¥ã¼ã® "Assign Residue..." ã³ãã³ããä½¿ããã¨ã§ãã +

+ + + +

+ +

2. Bond/Angle/Dihedral/Improper ãã¼ãã«

+ +

3. ãã©ã¡ã¼ã¿ãã¼ãã«

+ãã©ã¡ã¼ã¿ãã¼ãã«ã¯ãåååå¦ãã©ã¡ã¼ã¿ãè¡¨ç¤ºãã¾ãã +

+ãã©ã¡ã¼ã¿ã¯ããã¤ãã®ç¨®é¡ã«ã°ã«ã¼ãåãããã¦ãã¾ãã"VDWs", "Bonds", "Angles", "Dihedrals", "Impropers", ããã¦ "VDW Pairs" ã§ãã +

+"Bonds" ãã©ã¡ã¼ã¿ã¯ã"k"ï¼çµåã®åã®å®æ°ãkcal/mol/Å²ï¼ã"r0"ï¼å¹³è¡¡çµåé·ããÅï¼ããæãã¾ãã"Angles" ãã©ã¡ã¼ã¿ã¯ã"k"ï¼çµåè§ã®åã®å®æ°ãkcal/mol/radian²ï¼ã"a0"ï¼å¹³è¡¡çµåè§ãdegreeï¼ããæãã¾ãã'Dihedrals", "Impropers" ãã©ã¡ã¼ã¿ã¯ã"k"ï¼åã®å®æ°ãkcal/mol/radian²ï¼ã"period"ï¼å¨æï¼ã"phi0"ï¼å¹³è¡¡äºé¢è§ãdegreeï¼ããæãã¾ãã"VDW Pairs" ãã©ã¡ã¼ã¿ã¯æ»å¤ã«ä½¿ããã¾ããããããååã®çµã¿åããã«ç¹æã® van der Waals ç¸äºä½ç¨ãè¨è¿°ãããã®ã§ã"eps", "r", "eps14", "r14" ããæãã¾ãã +

+ +

+ + + +

Step Six: Energy Minimization by Molecular Mechanics

1. About Molecular Mechanics Implementation in Molby

The molecular models built by hand generally include unnatural bond lengths, bond angles, van der Waals contacts, and so on. Molecular mechanics is a useful technique to remove such unnatural structures. @@ -748,7 +1106,7 @@ Following are the original papers published by the AMBER team. Please be sure to

Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollamn, P.A.; Case, D.A. Development and testing of a general Amber force field. J. Comput. Chem., 2004, 25, 1157â1174.

Wang, B.; Merz, K.M. Jr. A fast QM/MM (quantum mechanical/molecular mechanical) approach to calculate nuclear magnetic resonance chemical shifts for macromolecules. J. Chem. Theory Comput., 2006, 2, 209â215.

2. Energy Minimization How-to

Now we try energy minimization. We use 2,2'-dimethoxybiphenyl as an example.

@@ -756,66 +1114,67 @@ Now we try energy minimization. We use 2,2'-dimethoxybiphenyl as an example.

Build this molecule. The easiest way is, (1) double-click the empty editing area and type "C6H5C6H5", (2) select one ortho hydrogen, double-click, and type "OCH3", (3) repeat (2) for another ortho hydrogen on the other ring.

-Open the "MM/MD" menu, and select "antechamber/parmchk..." command in the "Tools" submenu. +Open the "MM/MD" menu, and select "Guess MM/MD Parameters..." command.

-A dialog like below shows up. Turn off the first two checkboxes. The "log" directory is used by AmberTools for storing intermediate files; the default value would be acceptable, but you can change it here. +A dialog like below shows up. This is for execution of Antechamber on the current molecule. Turn off the "Calculate partial charges" checkbox, and turn on the "Guess atom types" checkbox. The "log" directory is used by AmberTools for storing intermediate files; the default value would be acceptable, but you can change it here.

After pressing "OK", two dialog boxes appear in turn. They disappear so quickly that you may not recognize what they are saying; actually, the first one says "Running antechamber" and the second one "Running parmchk." These are programs included in AmberTools. In the present case, both programs complete successfully, and the following dialog appears.

Press "OK", and you will return to the molecule window. Do you notice what change has been made? It is the atom types that are modified. Specifically, the types of the atoms 0 and 10 are changed from "ca" to "cp".

If you are wondering what "ca" or "cp" mean, look at the global parameter table (MM/MD â View Global Parameters...), and find comment(s) in the "vdw" record.

Return to the molecule, and select MM/MD â Minimize.

A setting dialog opens. "Steps per frame" means the screen is updated every this number of steps. "Number of frames" means the maximum number of "frames" (i.e. screen updates) to calculate. If the minimization completes before this number of frames, the calculation will stop. The numbers 10 and 200 are reasonable choice in many cases.

-Press "OK", and minimization starts. As you expect, the dihedral angle between the two phenyl rings becomes large. The calculation will stop after 200 frames. You can see the number "199" at the right bottom of the window, and the slider at the bottom of the window is now active. Move the slider, and you can see how the molecular structure changed during the minimization. +Press "OK", and minimization starts. As you expect, the dihedral angle between the two phenyl rings becomes large. The calculation will stop after 200 frames. You can see the number "200" at the right bottom of the window, and the slider at the bottom of the window is now active. Move the slider, and you can see how the molecular structure changed during the minimization.

If you save this molecule at this stage, all the frames will be also saved (when you select the "mbsf" format), and the resulting file may be very large. If you do not want this, then you can remove all the frames by use of "Delete Frames..." command in the "Script" menu.

3. Handling electrostatic interaction

The above description is sufficient for initial cleanup of the molecular structure. However, we should go one further step to take electrostatic interaction into consideration. This is particularly important in molecules with polar functional groups (such as carbonyl).

-Continue our study on 2,2'-dimethoxybiphenyl. Open "MM/MD" â "Tools" â "Antechamber/parmchk...", and this time turn on the top checkbox. Also make sure the net molecular charge is correct. +Continue our study on 2,2'-dimethoxybiphenyl. Open "MM/MD" â "Guess MM/MD Parameters...", and this time turn on the top checkbox. Also make sure the net molecular charge is correct.

Press "OK", and calculation starts. This time the calculation should take much longer than before, because semi-empirical calculation is carried out for optimizing the structure and getting the partial charges.

When calculation is done, the molecular structure may change, because structure optimization has been done by semi-empirical calculation. However, even more important is the "charge" values. You can see the charge values by scrolling the table to the right. By use of these "charge" values, interaction energies of the polar functional groups can be taken into account.

-Note that the atomic charges given in the above method are derived from semi-empirical quantum chemical calculations. On the other hand, it is generally considered that the charges derived from ab initio calculations are better. Molby does not have capability to perform ab initio calculations, but it can help creating necessary input files for external quantum chemical programs. This will be described elsewhere in this User's Manual (not yet written, but coming soon). +Note that the atomic charges given in the above method are derived from semi-empirical quantum chemical calculations. On the other hand, it is generally considered that the charges derived from ab initio calculations are better. Molby does not have capability to perform ab initio calculations, but it can help creating necessary input files for external quantum chemical programs. This will be described elsewhere in this User's Manual.

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Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollamn, P.A.; Case, D.A. Development and testing of a general Amber force field. J. Comput. Chem., 2004, 25, 1157â1174.

2. ã¨ãã«ã®ã¼æå°åã®æ¹æ³

@@ -844,138 +1203,1684 @@ Molby ã®åååå¦è¨ç®ã¯ãåºæ¬çãªåååå ´ï¼çµåã®ä¼¸ç¸®ã

-"MM/MD"ã¡ãã¥ã¼ãéãã"Tools" ãµãã¡ãã¥ã¼ãã "Antechamber/parmchk..." ã³ãã³ããå®è¡ãã¾ãã +"MM/MD"ã¡ãã¥ã¼ãéãã"Guess MM/MD Parameters..." ã³ãã³ããå®è¡ãã¾ãã

"OK"ãæ¼ãã¨ãï¼ã¤ã®ãã¤ã¢ãã°ãé ã«ç¾ãã¾ããããã«æ¶ãã¦ãã¾ãã®ã§ãä½ã¨æ¸ãã¦ãããèªããªãããç¥ãã¾ãããæåã®ãã®ã¯ "Running antechamber", ï¼ã¤ãã®ãã®ã¯ "Running parmchk" ã¨æ¸ãã¦ããã¾ãããããã¯ AmberTools ã«å«ã¾ãã¦ããããã°ã©ã ã§ããä»ã®å ´åã¯ãä¸¡æ¹ã¨ãæ£ããå®è¡ãããæ¬¡ã®ãã¤ã¢ãã°ãç¾ãã¾ãã

"ca" ã "cp" ãä½ã®æå³ãç¥ããããã°ã"MM/MD" ã¡ãã¥ã¼ãã "View Global Parameters..." ãé¸ãã§ã¿ã¦ãã ãããMolby ã«åæ¢±ããã¦ãããã©ã¡ã¼ã¿ã®ä¸è¦§è¡¨ãåºã¦ãã¾ãã"vdw" ï¼van der Waals ãã©ã¡ã¼ã¿ã®æå³ã§ãããååã¿ã¤ãã®å®ç¾©ãå¼ãã¦ãã¾ãï¼ã®ä¸ã§ "ca", "cp" ãè¦ã¤ãã¦ãè¡¨ã®å³ç«¯ã«ããã³ã¡ã³ããè¦ã¦ã¿ã¦ãã ããã

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Step Five: Edit a Molecule: Using a Property Table

1. The Property Table of a Molecule

Step Seven: Molecular Dynamics (MD) Calculation

1. MD Calculation within Molby

-A molecule has many properties. It has a set of atoms and bonds. An atom has a name, an atom type, an element, a weight (which can be derived from the element), a charge, coordinates, and so on. According to the custom in the biomolecular modeling, atoms are grouped in "residues." It also has a set of parameters used in molecular mechanics. Molby also has a limited support for quantum chemical calculations. In relation to that, a molecule in Molby can retain extra information such as MO coefficients. +Molby implements molecular dynamics (MD) calculation which uses the same force fields as the energy minimization by molecular mechanics (MM). This implementation is suitable only for preliminary calculations (to check parameters quickly, etc.); for production runs, it is strongly recommended that you use one of the established software packages.

-Most of these information are accessible via the property table. The table is on the left side of the model window. +An example of preliminary MD run is presented here. We use 2,2'-dimethoxybiphenyl again. In a similar way as in the step six, create a model and assign MM parameters (including the partial charges on the atoms).

- -

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Step Six: Collaboration with Other Quantum Chemistry Softwares

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Step Seven: Using Embedded Ruby Interpreter

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Reference

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+Select MM/MD → Molecular Dynamics. A setting dialog opens. Although this dialog resembles that in MM minimization, it shows different parameters that are relevant to the MD calculation. +

+The "timestep" parameter defines the minimum time increment in solving the equation of motions. The "target temperature" defines the temperature of the system. Before running the MD calculation, all atoms are let to have random velocities with the Boltzmann distribution corresponding to the target temperature. In addition, the velocities are modified so that the temperature is kept constant. The "steps per frame" and "number of frames" parameters have the same meaning as in the MM minimization. The screenshot shows 10 as the "steps per frame"; this is an appropriate value for MM minimization, however for MD calculations a larger value would be more appropriate (like 100). +

+Pressing the "Advanced..." button opens another dialog with other parameters. The meanings of the parameters are described in the embedded Ruby document, in the MDArena page. +

+Return to the original MD dialog (by pressing "Close" in the advanced settings dialog), and press "OK". The MD run starts, and new frames are accumulated. If you find something is wrong, or want to stop before getting the specified number of frames, you can stop the MD run by pressing Command-period (Mac) or Control-period (Windows). +

2. Using Molby with AMBER: Creating Inputs and Importing Outputs

+For production runs, you can create AMBER input files from Molby. More specifically, you can create "prmtop" and "inpcrd" files for the SANDER module. +

+Note: There is no guarantee that Molby creates the exactly same input as the official AMBER modeling tools, nor the generated files are valid inputs for the SANDER module. You may need to modify them by hand. +

+To creat SANDER input files, select "Create SANDER input..." command in the "MM/MD" menu. +

+You will be asked first for the file name for the "prmtop" file. Please be sure to add ".prmtop" extension. The other file, "inpcrd" file, is created as the same name with the ".prmtop" extension replaced by the ".inpcrd" extension. +

+Subsequently, you will be asked to select one of the two versions of the prmtop files. The older one, "AMBER8/NAMD", allows you to use the output file by NAMD (see below). +

+Now you can transfer your files to the workstation running SANDER. To perform the simulation, you still need to create the instruction file for SANDER, which you should already know if you are using AMBER. +

+After the simulation is over, you can get the trajectory file ("mdcrd" file) back and import to Molby. Use "Import..." command in the "File" menu, select "AMBER mdcrd file (*.crd; *.mdcrd)", and specify the file. +

3. Using Molby with NAMD: Creating Inputs and Importing Outputs

+You can also use the NAMD software package for production run. NAMD is developed by the Theoretical Biophysics Group in the University of Illinois at Urbana-Champaign, and the official information is found at their web site (http://www.ks.uiuc.edu/Research/namd/). NAMD can use the AMBER "prmtop" as the input, by use of the instruction amber yes. See NAMD Users' Guide for details. +

+You can also import the NAMD output by importing the dcd file. The file format is also listed in the "Import..." file dialog. +

4. Building Solvated Structures

+When you want to perform MD simulations in explicit solvent, you need to build a box of solvent molecules around the target molecule. Molby can help creating solvated structures. +

+To build a solvated structure, you need to open the file containing the predefined box of the desired solvent. The following solvent box is included in the Molby package, and can be accessed from "File" → "Open Predefined" → "Solvent boxes" submenu. The tip3box was taken from the AmberTool package, and other solvent boxes were taken from Amber parameter database. +

+ + + + + + + + + + + + + + + + + +

name	solvent	reference
tip3pbox	water	Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. +J. Chem. Phys. 1983, 79, 926. +
chcl3box	chloroform	Cieplak, P.; Caldwell, J. W.; Kollman, P. A. +J. Comp. Chem. 2001, 22, 1048. +
dmsobox	dimethylsulfoxide	Fox, T.; Kollman, P. A. +J. Phys. Chem. B 1998, 102, 8070. +
meohbox	methanol	Caldwell, J. W.; Kollman, P. A. +J. Phys. Chem. 1995, 99, 6208. +
nmabox	N-methylacetamide	Caldwell, J. W.; Kollman, P. A. +J. Phys. Chem. 1995, 99, 6208. +

+While keeping the solvent box open, create or open the target (solute) molecule in a separate window. With this solute molecule in the front window, select "Solvate..." command in the "MM/MD" menu. +

+A dialog box opens. +

+In the popup menu "Choose solvent box:", you will find the solvent box you opened earlier. Note that this popup menu lists all open molecules that have the associated periodic box (or unit cell). This can lead to a confusing situation that, if you have another solvated structure also open, that structure will also be listed in this popup menu, because a solvated structure always have a periodic box. Therefore, please take care so that you choose the right solvent box.

+If you open the solvent box from the "Open Predefined" menu, you can easily recognize it in the popup menu, because the name has asterisks at the beginning and the end, like "*CHCl3*". +

+The "Box offset" parameters define the thickness of the solvent layer surrounding the solute molecule. More specifically, the periodic box of the solvated structure is determined as follows: the minimum cuboid that can surround the solute molecule is defined, and all the faces are offset by the "Box offset" distances to the outside direction. On the other hand, it is possible to define the size of the periodic box explicitly for any of the three (x, y, z) directions. If you wish to do this, give a negative number for that direction. (For example, if you want the periodic box to be 40 Å in the x direction, give -40 as the first "Box offset" parameter.) +

+The size of the periodic box can be checked by selecting "Xtal" → "Unit Cell..." menu command, or in the property table (the "unit cell" property). +

+The "Exclusion limit distance" defines the minimum allowed distance between the solvent and solute molecules. The solvent molecule is removed when it has atoms with smaller distances than this parameter from the solute molecule. +

+ +

ç¬¬ä¸æ®µéï¼ååååå¦è¨ç®

1. Molby çµã¿è¾¼ã¿ã®ååååå¦ (MD) è¨ç®

2. AMBER ã¨ã¨ãã«ä½¿ãï¼å¥åã®ä½æã¨åºåçµæã®ã¤ã³ãã¼ã

+SANDER ã®å¥åãã¡ã¤ã«ãä½ãã«ã¯ã"MM/MD" ã¡ãã¥ã¼ãã "Create SANDER input..." ã³ãã³ããé¸ãã§ãã ããã +

+æåã« "prmtop" ãã¡ã¤ã«ã®ååãèããã¾ããå¿ã ".prmtop" æ¡å¼µåãã¤ããããã«ãã¦ãã ãããããä¸ã¤ã® "inpcrd" ãã¡ã¤ã«ã¯ã".prmtop" ã ".inpcrd" ã«ç½®ãæããååã§ä¿åããã¾ãã +

+è¨ç®ãçµäºãããããã©ã¸ã§ã¯ããªãã¡ã¤ã« ("mdcrd" ãã¡ã¤ã«) ãåå¾ãã¦ãMolby ã«ã¤ã³ãã¼ããããã¨ãã§ãã¾ãã"File" ã¡ãã¥ã¼ã® "Import..." ã³ãã³ããé¸ã³ããã¡ã¤ã«ã¿ã¤ãã¨ãã¦ "AMBER mdcrd file (*.crd; *.mdcrd)" ãé¸ãã§ããã¡ã¤ã«ãèªã¿è¾¼ãã§ãã ããã +

3. NAMD ã¨ã¨ãã«ä½¿ãï¼å¥åã®ä½æã¨åºåçµæã®ã¤ã³ãã¼ã

+æ¬æ ¼çãªè¨ç®ãè¡ãããã« NAMD ãä½¿ããã¨ãã§ãã¾ããNAMD ã¯ã¤ãªãã¤å¤§å¦ã¢ã¼ããã»ã·ã£ã³ãã¼ã³æ ¡ã®çè«çç©ç©çã°ã«ã¼ããéçºããã½ããã¦ã§ã¢ããã±ã¼ã¸ã§ããå¬å¼ã¦ã§ããµã¤ãã¯ http://www.ks.uiuc.edu/Research/namd/ ã§ããNAMD ã¯ AMBER ã® "prmtop" ãå¥åã¨ãã¦ä½¿ããã¨ãã§ãã¾ãï¼amber yes å½ä»¤ãä½¿ãï¼ãè©³ããã¯ NAMD ã®ã¦ã¼ã¶ã¼ãºã¬ã¤ãããè¦§ãã ããã +

4. æº¶åªåæ§é ã®ä½æ

+æº¶åªåæ§é ãä½ãããã«ã¯ãã¾ãä½¿ç¨ããæº¶åªã®ç®±ãèªã¿è¾¼ãå¿è¦ãããã¾ããä»¥ä¸ã®æº¶åªã®ç®±ã Molby ã«åæ¢±ããã¦ããã"File" → "Open Predefined" → "Solvent boxes" ãµãã¡ãã¥ã¼ããé¸ã¶ãã¨ãã§ãã¾ããTip3box ã¯ AmberTool ããã±ã¼ã¸ããå¾ããã®ã§ãããä»ã®æº¶åªç®±ã¯ Amber parameter database ã§å¬éããã¦ãããã®ã§ãã +

+ + + + + + + + + + + + + + + + + +

name	solvent	reference
tip3pbox	water	Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. +J. Chem. Phys. 1983, 79, 926. +
chcl3box	chloroform	Cieplak, P.; Caldwell, J. W.; Kollman, P. A. +J. Comp. Chem. 2001, 22, 1048. +
dmsobox	dimethylsulfoxide	Fox, T.; Kollman, P. A. +J. Phys. Chem. B 1998, 102, 8070. +
meohbox	methanol	Caldwell, J. W.; Kollman, P. A. +J. Phys. Chem. 1995, 99, 6208. +
nmabox	N-methylacetamide	Caldwell, J. W.; Kollman, P. A. +J. Phys. Chem. 1995, 99, 6208. +

+ãã¤ã¢ãã°ãéãã¾ãã +

+"Open Predefined" ã¡ãã¥ã¼ããé¸ãã§éããæº¶åªç®±ã¯ããã«åºå¥ã§ãã¾ããååã®åå¾ã« * ãã¤ãã¦ããããã§ã ("*CHCl3*" ã®ããã«ï¼ã +

+"Box offset" ãã©ã¡ã¼ã¿ã¯ãæº¶è³ªååã®åããå²ãæº¶åªå±¤ã®åããæå®ãã¾ããè¨ãæããã¨ãããããä½æããæº¶åªåæ§é ã®å¨æå¢çã¯æ¬¡ã®ããã«æ±ºãããã¾ãï¼ã¾ãæº¶è³ªãå²ãæå°ã®ç´æ¹ä½ãç®åºããããããã®é¢ãå¤å´ã«åãã£ã¦ Box offsect ãã©ã¡ã¼ã¿åã ãç§»åããã¾ããä¸æ¹ãx, y, z ã®ããããã®æ¹åã«å¯¾ãã¦ãå¨æå¢çã®å¤§ãããæ±ºãããå ´åãããã¾ãããã®ã¨ãã¯ããã®æ¹åã® Box offset ãã©ã¡ã¼ã¿ã«è² ã®å¤ãæå®ãã¦ãã ãããï¼ãã¨ãã°ãx æ¹åã®å¨æå¢çãå¤§ããã 40 Å ã«ãããæã¯ã"Box offset" ã®æåã®ãã©ã¡ã¼ã¿ã -40 ã«ãã¦ãã ãããï¼ +

+å¨æå¢çã®ç®±ã®å¤§ããã¯ã"Xtal" → "Define Unit Cell" ã¡ãã¥ã¼ãé¸ã¶ã¨è¦ããã¨ãã§ãã¾ããã¾ããå±æ§ãã¼ãã«ã® "unit cell" ã§ãè¦ããã¾ãã

+"Exclusion limit distance" ã¯ãæº¶è³ªååã¨æº¶åªååã®ååéè·é¢ã®æå°å¤ãå®ãã¾ããæº¶åªååã®ããååãæº¶è³ªååãããã®è·é¢ä»¥åã«è¿ã¥ãã¦ããã¨ãããã®æº¶åªååã¯åãé¤ããã¾ãã +

+ +

+ + + +

Step Eight: MM/MD Calculation of Coordination Compounds

1. Use of UFF (Universal Force Field) Parameters

+Building molecular models of coordination compounds is often problematic. This is mainly due to the lack of appropriate MM parameters for metal atoms. One reasonable approach is to use UFF (universal force field) parameters developed by RappÃ© and coworkers (J. Am. Chem. Soc. 114, 10024-10035 (1992)). Although estimation of the UFF parameters from the molecular structure is rather complicated, it can be automated by computer programs. In the following, you will see how Molby can help modeling of coordination compounds with the UFF parameters. +

+Suppose we want to build a model of (terpy)PtCl, where terpy is 2,2':6',2"-terpyridine. +

+We need to build the molecular structure first. One approach is to build the organic part (terpy), and put metal atoms afterwards. Here, we will go through another route, namely start from the metal fragment and add ligands afterwards. In general, this approach should be more successful in building models of coordination compounds. +

+Select "Open Predefined..." menu item, and find "MX4 square-planar" like below. +

+A square planar fragment of "CuCl4" appears on the screen. +

+Choose the "Select" tool, double click on one of the chlorine atoms, and type "C6H5". +

+You see now a phenyl group is attached to the metal atom. The orientation of the phenyl ring needs to be fixed. Select the metal-C bond, and rotate the phenyl ring so that the ring is approximately coplanar with the metal-ligand plane. +

+Attach two other phenyl groups in a similay manner. +

+Remove the hydrogen atoms and create C-C bonds. Double-click on the carbon atoms connected to the metal, and change them to "N". Double-click on the metal atom and change it to "Pt". +

+Now the molecular structure is complete. Next we need to assign the MM parameters. To do this, select the "Guess UFF Parameters..." from the "MM/MD" menu. +

+A dialog like below opens up. Here are listed the atoms that are (1) the metal atoms, (2) the ligand atoms that are connected to the metal atoms, and (3) the ligand atoms that are connected to any of the atoms in (2). In other words, the atoms within "two-bonds" distances are shown in this dialog. The Pt atom is shown in red, because it does not have predefined MM parameters. The ligand atoms already have their MM parameters, but if you look closely not all atoms are correctly recognized. For example, the pyridine N atoms are incorrectly assigned as "n3", which is a sp3 nitrogen. +

+The UFF parameter estimation consists of two stages. The first stage is to assign the types of the ligand atoms. This is basically the same as the procedure described in Step 6, but this time we need to run Antechamber for the non-metal part only. By hitting the button "Run Antechamber for Non-Metal Fragment", Antechamber is executed for each non-metal fragments. You may need to assign the charge for each fragment; for example, if you are using catecholato ligand, that fragment should have charge of -2. +

+The fragment that are being assigned by Antechamber is shown in the main window as the selection. In this example, the first fragment contains only the chlorine atom, and the second fragment is the terpyridine ligand. +

+After running Antechamber, the table looks like below. Note that the values in the "type" column have been changed. +

+Next, we need to assign the "UFF types" to each atoms. In fact, the UFF types are already set in the previous stage. We still need to look at them, and correct the types if necessary. You can select the predefined UFF types from the popup menu. +

+Now we need to assign UFF parameters for the metal atoms. Click the button "Guess UFF Parameters for Bonds and Angles Including Metal Atoms". +

+Open the "Bonds" page, and check the columns "k" and "r0". You will find there the proposed values of force constant and equilibrium bond length, according to the UFF force field. If you find, by some reason, the values are not appropriate, then you can change them by hand. +

+You can check the "Angles" page as well. Check the columns "k" and "a0", for the force constant and equilibrium bond angle. Note that, in the case of square planar or octahedral metal center, there are "cis" and "trans" angles. The program will assign "trans" if the current bond angle is larger than 135 degree, and "cis" otherwise. So, if your starting geometry is not quite optimal, be careful to check the angle parameters. +

+Close this dialog, and go into MM/MD calculations as usual. For example, you can perform energy minimization and get the structure like below. +

2. Compounds Containing Metal-Ï Bonds

+Compounds containing metal-Ï bonds are also problematic in molecular mechanics calculations. The implementation of metal-Ï bonds in Molby is based on the proposal by Doman and coworkers (J. Am. Chem. Soc. 114, 7262-7272 (1992)). Herein we will see how to build a molecular model of ferrocene. +

+We start with the predefined structure "cyclopentadienyl." +

+Select the five carbon atoms, and do "Create Pi Anchor" menu command. +

+"Pi anchor" is a virtual atom, whose coordinates are defined as the center of mass of the "parent" atoms. In this case, the parent atoms of the pi anchor is the carbon atoms of the Cp ring. In the main screen, the pi anchor is shown as a green dot, and it is connected to the parent atoms by a green thin bonds. +

+Rotate the ring to show the "side view" of the ring, while keeping the pi anchor barely visible. Create a bond from the pi anchor to a new atom. Change the new atom to Fe. +

+Copy the cyclopentadienyl ring and the pi anchor, and paste in the same window. Place the new ring to the appropriate position, and bond the Fe atom and the new pi anchor. +

+Finally, make a bond between the two pi anchors. This is necessary to describe the barrier for ring rotation. The anchor-anchor bond is shown as a half-transparent green stick. +

The ring rotation can be described as a dihedral term in the form of "ring atom"-"pi anchor"-"metal"-"X". However, in the case of a linear metallocene, "X" is the other pi anchor. Since the "pi anchor"-"metal"-"pi anchor" angle is always close to 180 degree, the dihedral angle cannot be defined. For this reason, the linear metallocene requires special treatment of the dihedral term in the form of "ring atom"-"pi anchor"-"pi anchor"-"ring atom". That is why we need to make a bond between two pi anchors. This is not the case for the bent metallocenes (like Cp₂TiCl₂), or half-sandwich complexes. +

+Now we can go on to the UFF dialog as before. This time, we skip the "non-metal fragments" part, because Antechamber cannot handle cyclopentadienyl anion. Our cyclopentadienyl ring already has correct atom types, so we will use them as they are. +

+Change the UFF type of the Fe atom to "Fe2+ octahedral". +

+Click on the "Bonds" label, and change the "r0" parameter of the two bonds of "##-fe" or "fe-##" type ("##" represents the pi anchor). This should be the metal-pi distance, which is 1.66 Å for ferrocene. +

+The "Angle" page should also be edited. The "a0" parameter is set to 90.0 for the "fe-##-ca" type angles (ten lines from the top), and 180.0 for the "##-fe-##" type angle (the last line). +

+Hit the "Guess UFF Parameters..." button to complete the calculation of the UFF parameters. +

+You can now try the MM/MD calculation. Energy minimization results in an eclipsed conformation. MD at 298K shows that the Cp rings freely rotate at this temperature. +

ç¬¬å«æ®µéï¼éä½ååç©ã®MM/MDè¨ç®

1. UFF (Universal Force Field) ãã©ã¡ã¼ã¿ãä½¿ã

+éä½ååç©ã®ååã¢ãã«ä½æã«ã¯ããããåé¡ãããã¾ããä¸»ãªåé¡ã¯ãéå±ååã®åååå¦ãã©ã¡ã¼ã¿ãç¨æããã¦ããªããã¨ã§ããä¸ã¤ã®åççãªæ¹æ³ã¯ãRappÃ©ãã«ãã£ã¦ææ¡ããã UFF (universal force field) ãã©ã¡ã¼ã¿ãä½¿ããã¨ã§ã (J. Am. Chem. Soc. 114, 10024-10035 (1992))ã ååæ§é ãã UFF ãã©ã¡ã¼ã¿ãè¦ç©ããã®ã¯ããè¤éãªä½æ¥ã§ãããããã°ã©ã ã«ãã£ã¦èªååãããã¨ã¯å¯è½ã§ããä»¥ä¸ã«ãUFF ãç¨ããéä½ååç©ã®ã¢ãã«ã³ã°ã« Molby ãã©ã®ããã«å©ç¨ã§ããããç¤ºãã¾ãã +

+ä¾ã¨ãã¦ã(terpy)PtCl ã®ååã¢ãã«ãä½ã£ã¦ã¿ã¾ããããterpy ã¯ 2,2':6',2"-terpyridine ã§ãã +

+"File" ã¡ãã¥ã¼ãã "Open Predefined..." ãé¸ã³ãä¸ã®ããã« "MX4 square-planar" ãè¦ã¤ãã¦ãã ããã +

+å¹³é¢åéä½ã® "CuCl4" æ§é ãç¾ãã¾ãã +

+ä»ã®ï¼ã¤ã®å¡©ç´ ååãåæ§ã«ãã§ãã«åºã«ç½®ãæãã¾ãã +

+æ°´ç´ ååãåé¤ãã¦çç´ âçç´ çµåãä½æãã¾ãããããããéå±ã«çµåãã¦ããçç´ ååãããã«ã¯ãªãã¯ãã¦ã"N"ååã«å¤ãã¾ããéå±ååãããã«ã¯ãªãã¯ãã¦ã "Pt" ã«å¤ãã¾ãã +

+ããã§ååæ§é ã¯ã§ããããã¾ãããæ¬¡ã«ãåååå¦ãã©ã¡ã¼ã¿ãè¨å®ãã¾ãã"MM/MD"ã¡ãã¥ã¼ãã "Guess UFF Parameters..." ã³ãã³ããé¸æãã¾ãã +

+Antechamber ãèµ°ãããã¨ãè¡¨ã¯ä¸ã®ããã«ãªãã¾ãã"type" åã®å¤ãå¤ãã£ã¦ãããã¨ã«æ³¨æãã¦ãã ããã +

+æ¬¡ã«ãåååã® "UFF type" ãè¨å®ãã¾ããåã®æ®µéã§ UFF type ãä»®ã«è¨å®ãã¦ããã¾ãããä¸éãè¦ç´ãã¦ãå¿è¦ãªãå¤æ´ãã¦ãã ãããUFF type ã¯ãããã¢ããã¡ãã¥ã¼ã§é¸æãããã¨ãã§ãã¾ãã +

+ +

+ä»åº¦ã¯ãéå±ååã®ãã©ã¡ã¼ã¿ãè¨å®ãã¾ãã"Guess UFF Parameters for Bonds and Angles Including Metal Atoms" ãã¿ã³ãæ¼ãã¦ãã ããã +

+"Bonds" ãã¼ã¸ãéãã¦ã"k" ã¨ "r0" ã®åãè¦ã¦ãã ãããUFF åååå ´ããäºæ¸¬ããããåã®å®æ°ãã¨ãçµåé·ããå¥ã£ã¦ããã¯ãã§ããä½ããã®çç±ã§ãå¤ãé©åã§ã¯ãªãã¨èããå ´åã¯ãæåã§å¤æ´ãããã¨ãã§ãã¾ãã +

2. éå±-Ï çµåãæã¤ååç©

+åååå¦è¨ç®ã§ã¯ãéå±-Ïçµåãæã¤ååç©ã®åãæ±ããåä»ã§ããMolby ã¯ãDoman ãã®æ¹æ³ (J. Am. Chem. Soc. 114, 7262-7272 (1992)) ã«æºãã¦éå±-Ïçµåã®åååå¦è¨ç®ãå®è£ãã¦ãã¾ããããã§ã¯ããã§ãã»ã³ã®ååã¢ãã«ãä½æãã¦ã¿ã¾ãã +

+"Open Predefined" ãã "cyclopentadienyl" ãé¸ã³ã¾ãã +

+ï¼ã¤ã®çç´ ååãé¸æãã"Create Pi Anchor" ã¡ãã¥ã¼ã³ãã³ããå®è¡ãã¾ãã +

+ç°ãåè»¢ããã¦ãæ¨ªããè¦ãåãã«ãã¾ããPi anchor ã¯ããããè¦ããããã«ãã¦ããã¾ããPi anchor ããçµåãåºãã¦ãæ°ããååãä½ãã¾ããæ°ããååã Fe ã«å¤ãã¾ãã +

+ã·ã¯ããã³ã¿ã¸ã¨ãã«ç°ã¨ pi anchor ãã³ãã¼ãã¦ãåãã¦ã£ã³ãã¦åã«ãã¼ã¹ããã¾ããæ°ããç°ã Fe ååãã¯ããã§åå¯¾å´ã«ç§»åããæ°ãã pi anchor ã¨ Fe ååãçµåããã¾ãã +

+Fe ã® UFF ã¿ã¤ãã "Fe2+ octahedral" ã«å¤æ´ãã¾ãã +

+"Bonds" ã©ãã«ãã¯ãªãã¯ãã"##-fe" ã¾ãã¯ "fe-##" ã¿ã¤ãã®çµåã® "r0" ãã©ã¡ã¼ã¿ã®å¤ãå¤æ´ãã¾ãï¼"##" ã¯ pi anchor ãæå³ãã¾ãï¼ããã®å¤ã¯éå±-Ïçµåã®è·é¢ã§ãããã§ãã»ã³ã®å ´åã¯ 1.66 Å ã«ãªãã¾ãã +

+"Guess UFF Parameters..." ãã¿ã³ãæ¼ãã¦ãUFF ãã©ã¡ã¼ã¿ã®è¨ç®ãè¡ãã¾ãã +

+ããã§ MM/MD è¨ç®ãè©¦ããã¨ãã§ãã¾ããã¨ãã«ã®ã¼æå°åãè¡ãã¨ãéãªãåã®éç½®ãå¾ããã¾ãã298K ã§ MD ãè¡ãã¨ãCp ç°ããã®æ¸©åº¦ã§èªç±åè»¢ãã¦ãããã¨ããããã¾ãã +

+ +

+ + + +

Step Nine: Collaboration with Other Quantum Chemistry Softwares

+Molby has a capability to export and import files for quantum chemistry softwares, namely Gaussian and GAMESS. At present, the capability is quite limited, and in many cases it would be much better to use other established softwares. Nevertheless, if you are already familiar with Molby, you may want to use Molby for creating input files for Gaussian and GAMESS and processing outputs. Here are instructions how to do it. +

+Needless to say, you need to have access to Gaussian or GAMESS program packages. They can be on the same machine or on other machines (workstations) than Molby. Please learn how to use these packages before using Molby as described in this section. +

1. Using Gaussian

+The Gaussian input can be created by selecting "Export..." command in the "File" menu. The file extension is either "gjf" (as is the convention in GaussianW) or "com" (as in UNIX version of Gaussian). +

+The output will look like this. Although Molby can create only one type of Gaussian input (optimize with PM3), it should be relatively easy to modify the generated input file by hand. +

%Chk=benzene.chk +# PM3 Opt + + unnamed1; created by Molby at Sat Feb 11 00:30:21 +0900 2012 + + 0 1 +C -0.653000 0.585000 -1.068000 +H -1.158000 1.039000 -1.898000 +C 0.729000 0.607000 -1.003000 +H 1.295000 1.076000 -1.783000 +C 1.382000 0.021000 0.069000 +H 2.452000 0.038000 0.119000 +C 0.651000 -0.586000 1.076000 +H 1.156000 -1.039000 1.906000 +C -0.732000 -0.607000 1.012000 +H -1.298000 -1.077000 1.792000 +C -1.384000 -0.021000 -0.060000 +H -2.455000 -0.038000 -0.110000 + +

+When you do geometrical optimization, you may want to examine how the structure changes as the calculation proceeds. This can be done by importing the Gaussian output file. The extention should be either ".out" or ".log". +

2. Using GAMESS

+Creating GAMESS input can be more complicated than Gaussian, so that Molby provides a simple dialog to help creating GAMESS input. The dialog is accessible from the "Creating GAMESS input..." command in the "QChem" menu. +

+You can specify various settings in the dialog. +

SCF Type: RHF, ROHF, or UHF.
Run Type: Energy, Property, or Optimize.
Use internal coordinates for structure optimization: Add instructions for automatic generation of internal Z-matrix. (Note: It cannot be used for linear molecules.)
Charge: The (formal) charge of the molecule.
Multiplicity: The spin multiplicity.
Use DFT: Check if you want to use DFT.
DFT type: At present only B3LYP is available in this dialog.
Basis set: One of PM3, STO-3G, 3-21G, 6-31G, 6-31G(d), 6-31G(d, p), 6-311G, 6-311G(d, p), or LanL2DZ.
Load Basis Set: Additional basis set can be imported from a file. The file should be in the GAMESS standard format. See the "basis_sets" directory in the "Script" directory for examples.
Use secondary basis set: Check if you want to use another basis set for certain elements.
Elements: The elements (comma separated) to use secondary basis set.
Basis set: The secondary basis set.
Calculate electrostatic potential: This is used for RESP charge calculation for AMBER.
Include NBO instructions: When GAMESS is built with NBO (natural bond orbital) support, these checkboxes generate instructions for running NBO program for the designated properties.
Execute GAMESS on this machine: (0.6.5 and later) Execute GAMESS, provided that GAMESS is installed on the same computer. Specify the full path of the GAMESS executable in "Path", and the number of CPU cores for calculation in "N of CPUs."
+(Note: GAMESS may not work depending on the version of the executable.)

+When the calculation of GAMESS is complete, you will find two output files, namely *.log and *.dat. Either format can be imported by use of the "Import..." menu command. Some informations are included in both (e.g. coordinates during structural optimization), but other informations are only in one of these files (e.g. the full description of gaussian functions is only in the *.log file, whereas the orbital coefficients with full precision are only in the *.dat file). You need to be familiar with the structure of the GAMESS output files to fully utilize the GAMESS import capability of Molby. +

3. Using GAMESS for calculation of the RESP charges

+We already saw how to assign partial charges for evaluation of electrostatic interactions in MM calculations. There we used semi-empirical calculations, although ab initio calculations will give better results if possible. Here are instructions how to do it using GAMESS. +

+Select "MM/MD" → "GAMESS/RESP...". +

+The following window pops up. As the first step, press the "Create GAMESS Input..." button. +

+The familiar GAMESS dialog opens up. It is most important to turn on the "Calculate electrostatic potential (ESP)" checkbox (it should be turned on if you follow the steps as described here, but please double-check). Also make sure that the charge and multiplicity are correct, and select a suitable basis set (6-31G(d) is recommended). +

+Press OK to create the GAMESS input, and send it to GAMESS. The calculation will take time, so that you can finish Molby (after saving the molecule as a msbf file!), and work on something else at this stage. +

+After the GAMESS calculation is complete, open the same molecule, and select "MM/MD" → "Tools" → "GAMESS/RESP..." again. This time, follow the second step by pressing the "Import GAMESS dat..." button. +

+Select the GAMESS dat file (which should be available when the GAMESS calculation ends successfully), and import it. When the import is complete, the "Run RESP..." button should be enabled. If it does not, the imported dat file does not have the electrostatic potential information. Start over from the step 1, and make sure that the "Calculate electrostatic potential (ESP)" checkbox is on. +

+Press the "Run RESP..." button, and the following dialog opens. This is almost the same as the dialog for Antechamber described before. +

+Press the "OK" button, and the RESP charge will be assigned to the atoms. +

ç¬¬ä¹æ®µéï¼ä»ã®éååå¦ã½ããã¦ã§ã¢ã¨ã®é£æº

+Molby ã¯éååå¦è¨ç®ã½ããã¦ã§ã¢ GaussianãGAMESS ã®ãã¡ã¤ã«ãä½æï¼èªã¿è¾¼ã¿ããæ©è½ãæã£ã¦ãã¾ããç¾ç¶ã§ã¯ãMolby ã«ã¯æ¥µãã¦å¶éãããæ©è½ãããªããããããããä»ã®å®ç¸¾ããã½ããã¦ã§ã¢ãä½¿ã£ãæ¹ãããã§ããããããããMolby ã®æä½ã«æ£ãã¦ãããªããGaussian ã GAMESS ã®å¥åãä½æãã¦çµæãèªã¿è¾¼ãã®ã« Molby ãä½¿ããããã¨ãããããããã¾ãããã©ã®ããã«ããã°ããããèª¬æãã¾ãã +

1. Gaussian ãä½¿ã

+Gaussian ã®å¥åã¯ "File" → "Export..." ã³ãã³ããä½¿ãã°ä½æãããã¨ãã§ãã¾ãããã¡ã¤ã«ã®æ¡å¼µåã¯ "gjf"ï¼GaussianW ã§ã®ç¿æ£ï¼ãã¾ãã¯ "com"ï¼UNIX çã§ã®ç¿æ£ï¼ã§ãã +

2. GAMESS ãä½¿ã

+GAMESS ã®å¥åãä½æããã®ã¯ Gaussian ããããã£ã¨è¤éãªã®ã§ãå°ç¨ã®ãã¤ã¢ãã°ãç¨æããã¦ãã¾ãããã®ãã¤ã¢ãã°ã¯ã"QChem" → "Creating GAMESS input..." ã³ãã³ãã§éããã¨ãã§ãã¾ãã +

+ãã®ãã¤ã¢ãã°ã§ã¯ããããããªè¨å®ãæ±ºãããã¨ãã§ãã¾ãã +

SCF Type: RHF, ROHF, ã¾ãã¯ UHF.
Run Type: Energy, Property, ã¾ãã¯ Optimize.
Use internal coordinates for structure optimization: åé¨çã« Z-matrix ãèªåçæããããã®å½ä»¤ãä»ãå ãã¾ããï¼æ³¨ï¼ ç´ç·ç¶ååã«ã¯ä½¿ãã¾ãããï¼
Charge: ååã®å½¢å¼é»è·ã
Multiplicity: ã¹ãã³å¤éåº¦ã
Use DFT: DFT è¨ç®ãè¡ãã¨ããã§ãã¯ãã¾ãã
DFT type: ãã®ãã¤ã¢ãã°ã§ã¯ B3LYP ã®ã¿æå®ã§ãã¾ãã
Basis set: ä»¥ä¸ã®åºåºãæå®ã§ãã¾ãï¼PM3, STO-3G, 3-21G, 6-31G, 6-31G(d), 6-31G(d, p), 6-311G, 6-311G(d, p), ã¾ãã¯ LanL2DZ.
Load Basis Set: ãã¡ã¤ã«ããè¿½å ã®åºåºé¢æ°ãèªã¿è¾¼ã¿ã¾ãããã¡ã¤ã«ã¯ GAMESS ã®æ¨æºçãªãã©ã¼ãããã«å¾ã£ã¦ããå¿è¦ãããã¾ãããã¡ã¤ã«ã®ä¾ã¨ãã¦ã"Scripts" ãã£ã¬ã¯ããªã®ä¸ã® "basis sets" ãã£ã¬ã¯ããªãè¦ã¦ã¿ã¦ãã ããã
Use secondary basis set: ç¹å®ã®åç´ ã®ã¿å¥ã®åºåºãä½¿ãããã¨ããã§ãã¯ãã¾ãã
Elements: å¥ã®åºåºãä½¿ãåç´ ï¼ã³ã³ãã§åºåã£ã¦è¤æ°æå®ã§ãã¾ãï¼ã
Basis set: å¥ã®åºåºã
Calculate electrostatic potential: RESP é»è·ãæ±ããããã®éé»ããã³ã·ã£ã«ã®è¨ç®ãè¡ãã
Include NBO instructions: GAMESS ã NBO (natural bond orbital) ããµãã¼ããã¦ããå ´åã¯ããããã®ãã§ãã¯ããã¯ã¹ã§æå®ãããã®ã NBO ããã°ã©ã ã§è¨ç®ãããããã«ãã³ãã³ããçæãã¾ãã
Execute GAMESS on this machine: (0.6.5 ä»¥é) Molby ã¨åãã³ã³ãã¥ã¼ã¿ã« GAMESS ãã¤ã³ã¹ãã¼ã«ããã¦ããã¨ããGAMESS ãå®è¡ãããã¨ãã§ãã¾ããPath ã« GAMESS ã®å®è¡ãã¡ã¤ã«ã®ãã«ãã¹åãN of CPUs ã«ä½¿ç¨ãã CPU ã®ã³ã¢æ°ãæå®ãã¾ãã
+ï¼æ³¨ï¼ GAMESS ã®ãã¼ã¸ã§ã³ã«ãã£ã¦ã¯åä½ããªããã¨ãããã¾ããï¼

3. GAMESS ãç¨ãã¦ RESP é»è·ãè¨ç®ãã

+ã¡ãã¥ã¼ãã "MM/MD" → "GAMESS/RESP..." ãé¸ã³ã¾ãã +

+æ¬¡ã®ã¦ã£ã³ãã¦ãéãã¾ããç¬¬ï¼ã®ã¹ãããã¨ãã¦ã"Create GAMESS Input..." ãã¿ã³ãæ¼ãã¾ãã +

+GAMESS ã®ãã¤ã¢ãã°ãéãã¾ããå¤§åãªã®ã¯ã"Calculate electrostatic potential (ESP)" ãã§ãã¯ããã¯ã¹ããªã³ã«ãããã¨ã§ãï¼ããã®æé ã«å¾ãã°ãèªåçã«ãªã³ã«ãªã£ã¦ããã¯ãã§ãããä¸å¿ç¢ºèªãã¦ãã ããï¼ãååã®é»è·ã»ã¹ãã³å¤éåº¦ãæ£ãããã¨ãç¢ºããï¼åºåºé¢æ° (6-31G(d) ããããã) ãæå®ãã¦ãã ããã +

+OK ãã¿ã³ãæ¼ãã¦ GAMESS å¥åãä½æããGAMESS ã§è¨ç®ãå®è¡ãã¦ãã ãããè¨ç®ã«ã¯æéããããã¾ãããããã®æç¹ã§ Molby ãçµäºãã¦ä»ã®ä½æ¥ããã¦ããã ãã¦æ§ãã¾ããï¼ãã ããååãã¡ã¤ã«ã mbsf å½¢å¼ã§ä¿åãããã¨ãå¿ããªãã§ï¼ï¼ã +

+GAMESS è¨ç®ãå®äºããããåãååãã¡ã¤ã«ãéãã"MM/MD" → "Tools" → "GAMESS/RESP..." ãããä¸åº¦é¸æãã¦ãã ãããä»åº¦ã¯ãç¬¬ï¼ã¹ãããã® "Import GAMESS dat..." ãã¿ã³ãæ¼ãã¾ãã +

+GAMESS ã® dat ãã¡ã¤ã«ãé¸æãï¼GAMESS ã®è¨ç®ãæåããã°ãããã§ãã¦ããã¯ãã§ãï¼ãèªã¿è¾¼ãã§ãã ãããèªã¿è¾¼ã¿ãå®äºãããã"Run RESP..." ãã¿ã³ãæå¹ã«ãªã£ã¦ããã¯ãã§ãããããããªããªãã£ãããèªã¿è¾¼ãã dat ãã¡ã¤ã«ã«éé»ããã³ã·ã£ã«ã®ãã¼ã¿ãå«ã¾ããªãã£ãã¨ãããã¨ã§ããããä¸åº¦ç¬¬ï¼ã¹ãããããããç´ããç¹ã« "Calculate electrostatic potential (ESP)" ãã§ãã¯ããã¯ã¹ããªã³ã«ãªã£ã¦ãããã¨ãç¢ºããã¦ãã ããã +

+"Run RESP..." ãã¿ã³ãæ¼ãã¨ãæ¬¡ã®ãã¤ã¢ãã°ãéãã¾ããããã¯ãåã«èª¬æãã Antechamber ã®ãã¤ã¢ãã°ã¨ã»ã¨ãã©åãã§ãã +

+ +

+ + + +

Step Ten: Working with Crystal Structures

+Information obtained from single-crystal X-ray analysis is a very important source of molecular structure. Molby can import crystallographic information files (CIFs) and handle structural data included in them. Although Molby does not have capability of solving structures from diffraction data, it does provide convenient features for viewing and examining crystal structures. +

1. Importing a CIF file

+Select "Open..." menu command in the "File" menu, and choose "Crystallographic Information File (CIF)" as the file type. +

+Select a CIF file and hit "Open". If the molecule has crystallographic symmetry, it should have bonds including symmetry related atoms. In this case, a dialog like below is shown and you are asked how to handle such bonds. +

+If the molecule is discrete with an imposed crystallographic symmetry, the default selection (the second one) should work all right. In other cases, where the molecule is an infinite chain, the first choice may make more sense. Expansion by symmetry is also available as a separate command, so it is also safe to ignore extra bonds at this stage (the third choice) and do symmetry expansion later. +

+After expansion, the molecule looks like this. The atoms with darker colors are "expanded atoms." +

+Molby internally handles all atomic positions as cartesian coordinates. However, the fractional coordinates can be calculated "on-the-fly." In the property table, you can choose to display the fractional coordinates (together with the site occupancies and isotropic temperature factors) as below. +

+ +

2. Examining the Crystal Structure

+Commands for examining the crystal structure are available in the "Xtal" menu. +

2-1. Unit Cell

+The "Unit Cell" command is used to set the unit cell parameters. It is also possible to set the origin and the unit cell axes directly. +

2-2. Symmetry Operation

+The "Symmetry Operation" command is used to add/remove the symmetry operation, or change the space group. +

+Hitting the "Select..." button causes another dialog to open, where you can choose one of the predefined space groups. All 230 space groups are included with various origin and axis settings (not all possible choices are covered though). +

2-3. Symmetry Expansion

+The "Complete by Symmetry" command is used to expand the molecular fragment in the asymmetric unit. It is supposed to work similarly as the "expand fragments" option in loading CIFs, but the result may be different. (This is because, in the "Complete by Symmetry" command, the bonds between different asymmetric units are "guessed" based on interatomic distances instead of being read from the CIF file.) +

+The "Create Packing Diagram" command generates symmetry-related atoms within the given range of the fractional coordinates. +

+The "Show Periodic Image" command does not generate new atoms, but shows the periodic images of the present unit cell. +

+The "Remove Expanded Atoms" command removes the atoms generated by symmetry expansion. There are two options; one is to remove all expanded atoms, and the other is to remove only those atoms that are included in completely expanded fragments (i.e. the fragments containing at least one non-expanded atoms will be kept unchanged). +

+The result looks like below. Note that the periodic images are still shown, because they are not expanded atoms but just images shown on the screen. +

+ +

2-4. Bonds, Angles, and Planes

+The "Bonds and Angles with Sigma..." command is used to calculate the interatomic distances and angles with the standard deviations. +

+Hit "Add Bond" or "Add Angle" button to create a new entry, then select the atoms one by one in the main window. After adding one "bond" and one "angle", the window looks like below. Note that you can choose atoms that are not connected via chemical bonds. +

+To use the calculated information in other applications (like pasting into a word processor), select the table rows and hit "Export to Clipboard." The information is copied as a plain text (one line per row) that can be pasted into other applications. +

+The "Best-Fit Planes" command is used for calculating mean planes, angles between the planes, and distances of atoms from the plane. After the dialog is opened, the set of atoms can be assigned by selecting the atoms in the main window and hit one of the "Set Current Selection" buttons. +

+ +

2-5. ORTEP Drawing

+The "Show ORTEP" command open the dialog like below. +

+The ORTEP drawing is created by the bundled ORTEP-III program. The following citation should be made when using the output. +

+Burnett, M. N.; Johnson, C. K. ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations, Oak Ridge National Laboratory Report ORNL-6895, 1996. +

+On this dialog, you can choose the appearance of the atoms and bonds. The orientation of the drawing is similar (although not completely the same) as in the main window. The drawing can be exported as an ORTEP input file or a graphic file (either as an encapsulated PostScript file, a PNG file or a TIFF file). When exporting to a bitmap file, the drawing is done at resolution of 360 dpi. +

ç¬¬åæ®µéï¼çµæ¶æ§é ãåãæ±ã

1. CIFãã¼ã¿ã®èªã¿è¾¼ã¿

+"File" ã¡ãã¥ã¼ãã "Open..." ã³ãã³ããé¸ã³ããã¡ã¤ã«ã¿ã¤ãã¨ãã¦ "Crystallographic Information File (CIF)" ãé¸æãã¾ãã +

+ +

2. çµæ¶æ§é ãèª¿ã¹ã

2-1. åä½æ ¼å

2-2. å¯¾ç§°æä½

+"Symmetry Operation" ã³ãã³ãã§ã¯ãå¯¾ç§°æä½ãè¿½å ã»åé¤ããããç©ºéç¾¤ãè¨å®ãããã§ãã¾ãã +

2-3. å¯¾ç§°æä½ã«ããæ¡å¤§

+"Create Packing Diagram" ã³ãã³ãã¯ãæå®ããé¨ååº§æ¨ã®ç¯å²ï¼æ¨æºã¯åä½æ ¼åå¨ä½ï¼ã«åå¨ããååãå¯¾ç§°æä½ã«ãã£ã¦çæãã¾ãã +

+"Show Periodic Image" ã³ãã³ãã¯ãæ°ããååãä½ãã®ã§ã¯ãªããåä½æ ¼åã®ç¹°ãè¿ãã¤ã¡ã¼ã¸ãç»é¢ä¸ã§è¡¨ç¤ºããããã®ãã®ã§ãã +

+çµæã¯ä¸ã®ããã«ãªãã¾ãã"Show Periodic Image" ã§è¡¨ç¤ºãã¦ããç¹°ãè¿ãã¤ã¡ã¼ã¸ã¯ã¾ã è¡¨ç¤ºããã¦ãããã¨ã«æ³¨æãã¦ãã ãããããã¯æ¡å¼µååã§ã¯ãªããããåé¤ã¯ããã¾ãããï¼ãã®ã¤ã¡ã¼ã¸ãæ¶ãã«ã¯ã"Show Periodic Image" ã³ãã³ãã§è¡¨ç¤ºãç¡å¹ã«ãã¦ãã ãããï¼ +

+ +

2-4. çµåã»è§åº¦ã»æé©å¹³é¢

+"Bonds and Angles with Sigma..." ã³ãã³ãã¯ãååéã®è·é¢ã»è§åº¦ãæ¨æºåå·®ä»ãã§è¨ç®ãããã®ã§ãã +

+"Best-Fit Planes" ã³ãã³ãã¯ãæé©å¹³é¢ãè¨ç®ããäºé¢è§ãååã»å¹³é¢éè·é¢ãè¨ç®ããã®ã«ä½¿ãã¾ãããã¤ã¢ãã°ãéããããæå®ãããååãã¡ã¤ã³ã¦ã£ã³ãã¦ã§é¸æãã¦ "Set Current Selection" ãã¿ã³ãæ¼ãã¦ãã ããã +

+ +

2-5. ORTEP æç»

+"Show ORTEP" ã³ãã³ãã¯ãä¸ã®ãããªã¦ã£ã³ãã¦ãéãã¾ãã +

+ORTEP æç»ã¯ãORTEP-III ããã°ã©ã ã§ä½æãã¦ãã¾ãããã®çµæãä½¿ãæã«ã¯ãä¸ã®ããã«å¼ç¨ãã¦ãã ããã +

+Burnett, M. N.; Johnson, C. K. ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations, Oak Ridge National Laboratory Report ORNL-6895, 1996. +

+ +

+ + + +

Step Eleven: Using Embedded Ruby Interpreter

+One of the most useful features of Molby is the embedded Ruby interpreter. When working on molecular modeling, it is often necessary to modify the model according to some mathematical relations. It is also convenient if we can extract some molecular information by automated "scripts" (i.e. computer programs), and export as a text file that can be processed by graphing software. The embedded Ruby interpreter is very useful under these circumstances. Actually, many functions of Molby itself are implemented by Ruby scripts. +

+To use the embedded Ruby interpreter in Molby, you need to be familiar with the Ruby programming language. You can find several good on-line tutorials in the Internet. However, you can also get the idea by going through the following sections. +

1. Using the Ruby Console

+The Ruby console window is open when Molby starts up. +

+On this window, you can execute Ruby scripts in an interactive manner. Let us try something on it now. Make the console window active by clicking on it, and type "1+2" followed by hitting the Return key. You will find this: +

% 1+2 +--> 3 +% +

+The Ruby interpreter calculated "1+2", and displayed the answer (3) in the following line. +

+You can give a longer expression including parenthesis. +

% (13.0*13.0+7.0*7.0)/1.365 +-->159.70695970696 +% +

+Or use common mathematical functions. +

% exp(-2.0) * (sin(0.25) + cos(0.25)) +-->0.1646105219232536 +% +

Usually in Ruby, you need to say Math.exp or Math.sin when using these mathematical functions. In Molby, the prefix Math is not necessary, because Molby automatically "includes" the Math module on startup.

+You can also use Strings, which is a series of characters. +

% "C" + "32" +-->"C32" +% +

+The "32" here is not a number but a string, because it is surrounded by quotation marks. If you omit these quotation marks, what happens? +

% "C" + 32 +

+Molby complains with this error dialog. It says "no implicit conversion of Fixnum into String," which means the integer 32 cannot be added to a string "C". Such kind of "type mismatch" error occurs very often, so please get used to it and learn how to fix it. +

+Another useful feature of Ruby is an Array, which is an ordered collection of other Ruby objects. An array is expressed by comma-separated values surrounded by a pair of brackets. +

% [1, 2, 3] +-->[1, 2, 3] +% +

+Any Ruby object can be stored in a variable. The name of variables should begin with a lowercase alphabet and should consist of alphabets, number characters and underline "_". +

% a = ["apple", "orange", "grape"] +-->["apple", "orange", "grape"] +% a[0] # This shows how to access the array elements +-->"apple" +

+ +

2. How to Handle Molecules in Molby Scripts

+The examples so far used only built-in types (Integer, String, Array) in Ruby, but you will definitely need to handle Molecules from your Molby scripts. Suppose we have a benzene molecule (again). +

+What if you want to convert it to chlorobenzene? There are two GUI ways; double-click on the H1 atom, and enter "Cl" into the dialog box, or double-click on the "H" text in the "element" column of the property table and change it to "Cl". But there is also a "Ruby" way, as follows: +

% atoms[1].element = "Cl" +-->"Cl" +% +

+This short piece of code implies some important concepts for coding in Molby. First, atoms denotes the atoms in the current molecule, which is the molecule in the frontmost window (except for the console window). atoms is not really an Array (as in the Ruby terminology), but can be used in a similar way as Array in many aspects. Specifically, it can be "indexed" to extract a specific atom. +

atoms[i] # Gives the i-th atom in the current molecule +

+Please make sure to say atoms[i], not atom[i]. This may be confusing, but it is because atoms is a collection of atoms and [] denotes "extraction of the i-th element." +

+The second point in the above example is .element = "Cl". In Ruby, a period (.) followed by a word (element) indicates a "method call." Method is a technical term in Ruby programming language; it is a function that is specific to an object. In this case, atoms[1] is an object, and it has a method named element= (including the last equal sign) whose meaning is "to change the element as indicated by the string value in the right side." In this way, the script atoms[1].element = "Cl" causes the element of the atom 1 changed to chlorine. +

+What if you want to change all hydrogen atoms to chlorine? Here is the code: +

% natoms.times { |i| if atoms[i].element == "H"; atoms[i].element = "Cl"; end } +-->12 +% +

+This is far more complicated than the previous example. A step-by-step explanation follows. +

+natoms gives the number of atoms in the current molecule as an integer number. This is actually a method call (natoms is a method of a Molecule object). Why a method is called even though no period is preceding the word? It is because Ruby has a feature called "implicit method call." This will be explained in more detail later. +

natoms # Gives 12 +

+times is a method of Integer (which is a built-in class of Ruby), which causes the following code surrounded by a pair of braces to be repeated the given number of times. +

natoms.times { ... } # { ... } is executed 12 times +

The code within the braces is called "block" in Ruby terminology.

+In the repeated code (or "block"), it is very likely that you want to know "how many times have I repeated?" This is achieved by declaring a variable name at the top of the block, surrounded by two vertical bars. +

natoms.times { |i| ... } # In { ... }, the variable i indicates the number of repeats +

+The following piece of codes is often used for testing. (puts prints the arguments to the console.) +

% natoms.times { |i| puts i } +0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +-->12 +

+The "12" in the last line is the "result value" of the method times, and the numbers 0 to 11 are the outputs from the puts method. Now you can see the block was executed 12 times with changing the variable i from 0 to 11. +

+In the block, there is an if statement: +

if atoms[i].element == "H"; atoms[i].element = "Cl"; end +

+The if statement has the following general form: +

if <condition>; <statements>; end +

+The <condition> is evaluated first, and if it is "true", the <statements> are executed; otherwise the <statements> are skipped. +

+Note: Ruby interprets only false and nil as non-true values. Other values are all "true". Specifically, the number 0 (zero) and an empty string ("") are evaluated to "true" (this is unlike other programming language such as Perl). Many Ruby methods returns nil in case of failure; such methods are suitable for the condition part. +

+Finally, the element method in the following code is different from the element= method that we previously used: +

atoms[i].element == "H" +

+In this case, the following symbol is "==", which means "are these equal?". This is distinct from the symbol "=", which means "the right side is assigned to the left side." The element symbol is interpreted as the element= method only when it is followed by the assignment symbol "=". The above code is not the case, so that it is interpreted as the element method, which returns the present element symbol as a String. +

+After execution of the script, the molecule should look like this: +

+ +

3. About the "Implicit" Method Call

+In the preceding section, we saw that natoms was a method of a Molecule object. +

natoms # 12, in case of benzene +

+Why this symbol natoms is regarded as a method call? Actually, when the Ruby interpreter finds a symbol beginning with a lowercase alphabet, it looks for a (local) variable first, and if none is found, then it assumes that the symbol is a method belonging to the "current object". Since Ruby is an object-oriented language, there is always a "current object", which is denoted as self. We can see it on our console: +

% self +-->Molecule["unnamed1"] +% +

+This piece of code indicates that the "current object" is a Molecule object. In fact, the Molecule object corresponding to the frontmost window becomes the "current object" when a script is executed on the Molby console. +

When no molecule is open, the "current object" is "main", which is the standard toplevel object in Ruby.

+Sometimes you happen to define a variable with the same name as a method of Molecule. In that case, access to the variable is preferred and the method is no longer called. +

% natoms = 2 # Define a variable +-->2 +% natoms # Now this is an access to the variable, not a method call +-->2 +% +

+In this situation, you can explicitly request a method call by specifying self. +

% self.natoms # This is a method call +-->12 +% +

+A special case is the methods with the assignment symbol ("="). For example, a method show_hydrogens= can control whether the hydrogen atoms are shown or not. However, without specifying self, the expression is always regarded as the assignment to a local variable. Therefore, self should be always explicitly given. +

% show_hydrogens = false # This does not change the Molecule's state, just changes a local variable +-->false +% self.show_hydrogens = false # This changes the Molecule's state +-->false +% +

4. Executing a Ruby Script on a File

+From the Ruby console, you can only execute a one-line script. For more complex scripts, or if you want to use the script many times over, it will be more convenient to store the script in a file and execute it. The "Execute Script..." command in the "Script" menu does this job. +

+There are endless possibilities for the script; here are presented only a few examples. The first script is to create a table of bond lengths including metal atoms (Fe): +

# Create a bond table including Fe +# Requires Molby +fp = open("bond_table.txt", "w") # Create an output file +atoms.each { |ap| # This is another way to repeat over all atoms; + # ap points to the atom on each iteration + if ap.element == "Fe" + r1 = ap.r # The cartesian coordinate of Fe + ap.connects.each { |n| # ap.connects is an array of atom indices connected to this atom + ap2 = atoms[n] # The atom connected to Fe + r2 = ap2.r # The cartesian coordinate of the atom + d = (r - r2).length # The bond length + fp.printf "%s-%s %.3f\n", ap.name, ap2.name, d # Write a table entry to the file + } # End loop (ap.connects) + end # End if +} # End loop (atoms.each) +fp.close # We are done with this file +

+Save this text to a file, select "Execute Script..." command (be sure that the target molecule is on the front), and choose the script file. After execution, a file named "bond_table.txt" will be generated in the same directory as the script file. +

+Here is another example, which works on a MD trajectory. For each frame, the molecule is reoriented so that the atom 0 is at the origin and atoms 1 and 2 are on the xy plane (with the atom 1 on the x-axis), and calculate the center of mass of the atoms 6 to 11. Such processing is useful to visualize how a particular part of the molecule moves around throughout the MD run. +

# Reorient the molecule and extract center of some group +# Requires Molby +fp = open("extract_group.txt", "w") # Create an output file +each_frame { |n| # This is an idiom to iterate over all frames + rotate_with_axis(1, 2, 0) # Reorientation of the molecule is so frequently used + # that the Molecule class has a method to do it + r = center_of_mass(6..11) # Also has a method to calculate the center of mass + fp.printf "%d %.6f %.6f %.6f\n", n, r.x, r.y, r.z # Write the coordinates +} +fp.close # We are done with this file +

+The last example generates a model of carbon nanotube with any chirality and length as you like. +

# Create a model of carbon nanotube +# Requires Molby +r = 1.42 # The C-C bond length +n = 10 # The default chirality index +m = 5 # (ibid) +aspect = 5.0 # The default aspect ratio (length / diameter) + +# Dialog to ask the chirality index and the aspect ratio +h = Dialog.run("Create Carbon Nanotube") { + layout(3, + item(:text, :title=>"Chirality Index"), + item(:textfield, :width=>80, :tag=>"n", :value=>n.to_s), + item(:textfield, :width=>80, :tag=>"m", :value=>m.to_s), + item(:text, :title=>"Aspect Ratio"), + item(:textfield, :width=>160, :tag=>"aspect", :value=>sprintf("%.1f", aspect)), + -1) +} + +exit if h[:status] != 0 +aspect = h["aspect"].to_f +n = h["n"].to_i +m = h["m"].to_i + +k = aspect / (PI * sqrt(3.0)) +points = [] +# The limiting points are (0, 0), (n, m), (k(n+2m), -k(2n+m)), (k(n+2m)+n, -k(2n+m)+n) +# Search for the lattice points that are within the parallelogram +# surrounded by the above points +# det is the determinant of the matrix that converts the unit cell to the above parallelogram +delta = 2 * k * (n * n + m * m + n * m) +(0..(k * (n + 2 * m) + n).ceil).each { |s| + ((-k * (2 * n + m)).floor..m).each { |t| + [0, 2.0/3.0].each { |d| # For two lattice points within the unit cell + ss = (k * (2 * n + m) * (s + d) + k * (n + 2 * m) * (t + d)) / delta + tt = (m * (s + d) - n * (t + d)) / delta + if ss >= 0.0 && ss < 1.0 && tt >= 0.0 && tt <= 1.0 + points.push([ss, tt, s, t]) # This point is within the parallelogram + end + } + } +} +# Create nanotube: line up [ss, tt] into cylindric shape +rad = sqrt(3.0) * r * sqrt(n * n + m * m + n * m) / (2 * PI) +len = rad * 2 * aspect +mol = Molecule.new +points.each { |p| + ap = mol.create_atom + ap.element = "C" + ap.atom_type = "ca" + ap.r = [rad * cos(2 * PI * p[0]), rad * sin(2 * PI * p[0]), len * p[1]] +} +mol.guess_bonds +# Show the result in a new window +mol2 = Molecule.open +mol2.add(mol) +

+ +

5. Where to Go from Here

+The embedded Ruby capability is very strong, and cannot be fully explained in this short tutorial. If you are interested, read carefully the reference of the Ruby extension. There are also many scripts in the Molby application, which you can examine by opening the "Scripts" folder (which is within the Application package in Mac OS X, and in the same folder as the Molby application in Windows). +

ç¬¬åä¸æ®µéï¼çµã¿è¾¼ã¿ Ruby ã¤ã³ã¿ããªã¿ãä½¿ã

1. Ruby ã³ã³ã½ã¼ã«ãä½¿ã

+Molby ãèµ·åããã¨ãRuby ã®ãã³ã³ã½ã¼ã«ã¦ã£ã³ãã¦ããéãã¾ãã +

% 1+2 +--> 3 +% +

+Ruby ã¤ã³ã¿ããªã¿ã "1+2" ãè¨ç®ããçã (3) ãæ¬¡ã®è¡ã«è¡¨ç¤ºããã¨ããã§ãã +

+ã«ãã³ãå«ãé·ãå¼ãè¨ç®ã§ãã¾ãã +

% (13.0*13.0+7.0*7.0)/1.365 +-->159.70695970696 +% +

+æ°å¦é¢æ°ãä½¿ããã¨ãã§ãã¾ãã +

% exp(-2.0) * (sin(0.25) + cos(0.25)) +-->0.1646105219232536 +% +

éå¸¸ Ruby ã§ã¯ããããã®æ°å¦é¢æ°ãä½¿ãã¨ãã«ã¯ Math.exp, Math.sin ã®ããã«æ¸ããªãã¦ã¯ãªãã¾ãããMolby ã§ã¯ãMath ã¨ããæ¥é è¾ã¯å¿è¦ããã¾ãããããã¯ Molby ãèµ·åæã« Math ã¢ã¸ã¥ã¼ã«ã "include" ããããã§ãã

+æåå (Strings) ãä½¿ããã¨ãã§ãã¾ãã +

% "C" + "32" +-->"C32" +% +

% "C" + 32 +

+Molby ã¯ã¨ã©ã¼ã¡ãã»ã¼ã¸ "no implicit conversion of Fixnum into String" ãè¡¨ç¤ºãã¾ããããã¯ããæ´æ°ã32 ããæååã"C" ã«è¶³ããã¨ã¯ã§ããªããã¨ãæå³ãã¦ãã¾ãããã®ãããªãåãéããã¨ã©ã¼ã¯ã¨ã¦ãããèµ·ããã®ã§ãã©ã®ããã«ç´ãã°ããããããçè§£ãã¦ããã¦ãã ããã +

% [1, 2, 3] +-->[1, 2, 3] +% +

% a = ["apple", "orange", "grape"] +-->["apple", "orange", "grape"] +% a[0] # éåã®è¦ç´ ãæå®ãã +-->"apple" +

+ +

2. Molby ã¹ã¯ãªããã§ååãæ±ã

+ããã¾ã§ã®ä¾ã§ã¯ãRuby ã®çµã¿è¾¼ã¿å Integer, String, Array ãä½¿ã£ã¦ãã¾ããããMolby ã¹ã¯ãªããã§ã¯ãååããæ±ããã¨ãå¿è¦ã«ãªãã¾ãããã³ã¼ã³ååãããã¨ãã¾ãããã +

% atoms[1].element = "Cl" +-->"Cl" +% +

atoms[i] # ç¾å¨ã®ååã® i çªç®ã®åå +

+atom[i] ã§ã¯ãªã atoms[i] ã§ãããã¨ã«æ³¨æãã¦ãã ãããæ··ä¹±ãã¾ãããããã¯ atoms ãååã®ä¸¦ã³ã§ [] ããâ¦çªç®ã®è¦ç´ ãåãåºããã¨ããæ©è½ãè¡¨ãããã§ãã +

+æ¬¡ã¯ .element = "Cl" ã§ããRuby ã§ã¯ãããªãªã (.) ã«ç¶ãã¦åèª (element) ãæ¸ãã¨ããã¡ã½ããå¼ã³åºããã«ãªãã¾ãããã¡ã½ãããã¨ã¯ããã°ã©ãã³ã°è¨èª Ruby ã®ç¨èªã§ãããå¯¾è±¡ï¼ãªãã¸ã§ã¯ãï¼ã«åºæã®åä½ãæãã¾ãããã®å ´åã¯ãatoms[1] ããªãã¸ã§ã¯ãã§ãelement= ã¨ããååã®ã¡ã½ãããæã£ã¦ãã¾ãï¼æå¾ã® '=' ãå«ã¿ã¾ãï¼ããã®ã¡ã½ããã¯ãããã®ååã®åç´ è¨å·ãå³è¾ºã®æååã§è¡¨ããããã®ã«å¤ãããã¨ããåãããã¾ãããã®ããã«ãã¦ãã¹ã¯ãªãã atoms[1].element = "Cl" ã¯ãååï¼ã®åç´ è¨å·ã Cl ã«å¤ãã¾ãã +

% natoms.times { |i| if atoms[i].element == "H"; atoms[i].element = "Cl"; end } +-->12 +% +

+ããã¯åã®ä¾ãããã£ã¨è¤éã§ããã¹ããããã¨ã«èª¬æãã¦ããã¾ãã +

natoms # 12 ã¨ãªã +

natoms.times { ... } # { ... } ã 12 åå®è¡ããã +

natoms.times { |i| ... } # { ... } ã®ä¸ã§ãå¤æ° i ã¯ç¹°ãè¿ãåæ°ãè¡¨ã +

% natoms.times { |i| puts i } +0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +-->12 +

+æå¾ã®è¡ã® "12" ã¯ãtimes ã¡ã½ããã®ãæ»ãå¤ãã§ãããã®ä¸ã® 0 ãã 11 ã®æ°ã¯ãputs ã¡ã½ããããã®åºåã§ãããããã¯ã 12 åå®è¡ãããå¤æ° i ã 0 ãã 11 ã¾ã§å¤åãããã¨ããããã¾ããã +

+ãããã¯ã®ä¸ã«ã¯ãif æãããã¾ãã +

if atoms[i].element == "H"; atoms[i].element = "Cl"; end +

+if æã®ä¸è¬å½¢ã¯æ¬¡ã®éãã§ãã +

if <æ¡ä»¶>; <å®è¡æ>; end +

+æå¾ã«åºã¦ãã element ã¡ã½ããã¯ãåã«åºã¦æ¥ã element= ã¡ã½ããã¨ã¯éãã¾ãã +

atoms[i].element == "H" +

+ã¹ã¯ãªãããå®è¡ããããååã¯æ¬¡ã®ããã«ãªãã¯ãã§ãã +

+ +

3. æé»ã®ã¡ã½ããå¼ã³åºã

+åã®ç¯ã§ãnatoms ã¯ Molecule ãªãã¸ã§ã¯ãã®ã¡ã½ããã§ãããã¨ãå¦ã³ã¾ããã +

natoms # 12 ï¼ãã³ã¼ã³ã®å ´åï¼ +

% self +-->Molecule["unnamed1"] +% +

+ãã®å ´åã§ããself ãæå®ããã°ã¡ã½ãããå¼ã³åºããã¨ãã§ãã¾ãã +

% self.natoms # ããã¯ã¡ã½ããå¼ã³åºã +-->12 +% +

% show_hydrogens = false # ããã¯ãã¼ã«ã«å¤æ°ã¸ã®ä»£å¥ã§ãååã®ç¶æã¯å¤ãããªã +-->false +% self.show_hydrogens = false # ããã¯ã¡ã½ããå¼ã³åºãã§ãååã®ç¶æãå¤ãã +-->false +% +

4. ãã¡ã¤ã«ä¸ã® Ruby ã¹ã¯ãªãããå®è¡ãã

+æ¬¡ã®ä¾ã¯ãMD ãã©ã¸ã§ã¯ããªãå¦çãããã®ã§ããåãã¬ã¼ã ã«å¯¾ãã¦ãåå 0 ãåç¹ãåå 1, 2 ã xy å¹³é¢ä¸ï¼åå 1 ã x è»¸ä¸ï¼ã«æ¥ãããã«ååãåéåãã¦ãåå 6 ãã 11 ã®éå¿ãè¨ç®ãã¾ãããã®ãããªå¦çã¯ãMD ã®çµæååã®ããé¨åãã©ã®ããã«åãããå¯è¦åããã®ã«ä¾¿å©ã§ãã +

+ +

5. æ¬¡ã«å¦ã¶ã¹ããã¨

+ +

+ + + +

Appendix

+ +

ä»é²

+ +

- +

Ruby Extension Reference

The following classes/module/exception are defined in the embedded Ruby interpreter in Molby. The methods defined in the module Kernel can be used as if they are builtin functions, like in the standard Ruby interpreter. All other classes and MolbyError exception are defined under the a module Molby. However, Molby:: prefix is not necessary because include Molby is invoked on startup.

+On startup, include Math is also invoked, so that the methods and constants in the Math module can also be used without prefix. +

It is recommended for you to read the document of the most important class Molecule. Follow the links as necessary, and you will understand how other classes are defined and used.

@@ -985,6 +2890,7 @@ It is recommended for you to read the document of the most important class Dialog

@@ -997,6 +2903,7 @@ It is recommended for you to read the document of the most important class Module

Kernel
Molby

Exception

+èµ·åæã«ã¯ include Math ãå¼ã³åºããããããMath ã¢ã¸ã¥ã¼ã«ã®ã¡ã½ãããå®æ°ãæ¥é è¾ãªãã§ä½¿ããã¨ãã§ãã¾ãã +

Dialog

DialogItem
IntGroup
LAMatrix
MDArena
MolEnumerable
Molecule

Module

Kernel
Molby

Exception

+ + + +

Filter Kit How-to

+In the research of chemistry, we sometimes a simple processing of text files. Ruby is particularly suitable for such purposes. To make the use of Ruby easier, Molby provides a special capability called "filter kit" (version 0.6.4 and later). The name originates from the "UNIX" culture, where small programs for text processing are called "filters". +

+Here is a description of making a filter script. As a demonstration, the filter here is a very simple function; it appends a sequential line number on each line. +

+To write a filter, we create a new text file, with extention ".rb" or ".mrb". Former is conventional as a Ruby script, but latter may be useful to specify Ruby scripts for Molby. +

+We start from the following line: +

Dialog.filter_kit("Filter Sample", "This is a sample filter.") { |args| +

+The method Dialog.filter_kit takes two arguments, the window title and the message. It also requires a block, which actually contains the main program. +

+When the user presses the "Select Files" button and choose files (which can be multiple), the block is executed with the array of the chosen file names as the argument. The block body is written as follows: +

1 Dialog.filter_kit("Filter Sample", "This is a sample filter.") { |args| + 2 args.each { |fname| + 3 fp = open(fname, "r") + 4 if fp == nil + 5 error_message_box("Cannot open file: #{arg}") + 6 next + 7 end + 8 puts fname + 9 a = fp.readlines + 10 fp.close + 11 File.rename(fname, fname + "~") + 12 fp2 = open(fname, "w") + 13 a.each_with_index { |ln, n| + 14 ln = (n + 1).to_s + " " + ln + 15 fp2.print ln + 16 } + 17 fp2.close + 18 } +

Line 2: The code in the following braces ({}) is repeated over all files.
Line 3: Open the file for reading.
Lines 4-7: If the file cannot be opened, then show the error message and continue to the next file.
Line 8: Display the filename as information. The output will be displayed in the text box within the filter dialog.
Line 9: Read all lines from the file and store in an array.
Line 10: Now we are done with this file, so close the file.
Line 11: Rename the file name with a tilda (~) at the end. (It is also possible to change the extension, for example; however, you need to learn about "regular expression" to write the code.)
Line 12: Open the file with the same name, this time for writing. We also need error handling for this operation as in line 4-7, which is omitted here for clarity.
Line 13: Repeat the following block (the code in the braces) for all elements in the array. The element and its index are given to the block as ln and n, respectively.
Line 14: Append the line number. (n + 1) denotes the line number (because the array index begins with zero), and to_s generates a String object from an Integer.
Line 15: Write the line to the file.
Line 17: Close the file.

+The above text is saved as "filter_sample.rb" (the filename can be arbitrary except for the extension). Open it with Molby, and you will get the filter running. +

Filter Kit ã®ä½¿ãæ¹

+åå¦ã®ç ç©¶ã§ã¯ãããã¹ããã¡ã¤ã«ã«ç°¡åãªå¦çãå ããããã¨ãã¨ãã©ãããã¾ããRuby ã¯ãã®ç®çã«ç¹ã«é©ãã¦ãã¾ããRuby ãç°¡åã«ä½¿ããããã«ãããããMolby ã¯ "filter kit" ã¨ããç¹å¥ãªæ©è½ãæã£ã¦ãã¾ãï¼ãã¼ã¸ã§ã³ 0.6.4 ä»¥éï¼ãFilter ã¨ããååã¯ "UNIX" ã®æåããæ¥ã¦ãããããã¹ããå¦çããå°ããªããã°ã©ã ã®ãã¨ãæãã¾ãã +

+ã¾ãæ¬¡ã®è¡ããå§ãã¾ãã +

Dialog.filter_kit("Filter Sample", "This is a sample filter.") { |args| +

2è¡: ä»¥ä¸ã®ãã¬ã¼ã¹ ({}) åã®ã³ã¼ããåãã¡ã¤ã«ã«å¯¾ãã¦ç¹°ãè¿ãã¾ãã
3è¡: ãã¡ã¤ã«ãèªã¿åãç¨ã«ãªã¼ãã³ãã¾ãã
8è¡: ãã¡ã¤ã«åãè¡¨ç¤ºãã¾ããåºåã¯ããã¤ã¢ãã°ã®ä¸ã®ããã¹ãããã¯ã¹ã«è¡¨ç¤ºããã¾ãã
9è¡: ãã¡ã¤ã«ã®ãã¹ã¦ã®è¡ãèªã¿è¾¼ãã§éåã«æ ¼ç´ãã¾ãã
10è¡: èªã¿è¾¼ã¿ãçµãã£ãã®ã§ããã¡ã¤ã«ãéãã¾ãã
11è¡: ãã¡ã¤ã«åã®å¾ãã«ãã«ã (~) ãã¤ãã¾ããï¼ãã¨ãã°æ¡å¼µåãå¤æ´ããããªã©ã®å¦çãå¯è½ã§ãããã³ã¼ããæ¸ãã«ã¯ãæ£è¦è¡¨ç¾ããå¦ã¶å¿è¦ãããã¾ããï¼
13è¡: ä»¥ä¸ã®ãããã¯ï¼ãã¬ã¼ã¹åã®ã³ã¼ãï¼ãéååã®ãã¹ã¦ã®è¦ç´ ï¼ã¤ã¾ããã¹ã¦ã®è¡ï¼ã«ã¤ãã¦ç¹°ãè¿ãã¾ããéåè¦ç´ ï¼ã¤ã¾ãããããã®è¡ï¼ã¨ãã®ã¤ã³ããã¯ã¹ããããã ln and n ã¨ãã¦ãããã¯ã«æ¸¡ããã¾ãã
14è¡: è¡çªå·ãã¤ãã¾ãã(n + 1) ãè¡çªå·ã«ãªãã¾ãï¼ã¤ã³ããã¯ã¹ã¯ï¼ããå§ã¾ãããï¼ãto_s ã¯æ´æ°ãæååã«å¤æãã¾ãã
15è¡: è¡ããã¡ã¤ã«ã«æ¸ãåºãã¾ãã
17è¡: ãã¡ã¤ã«ãéãã¦æ¸ãè¾¼ã¿ãå®çµãã¾ãã

+ +

Molby

An Interactive Molecular Modeling Softwarewith Integrated Ruby Interpreter

Version 0.5.5 build 20110721

Interactive Molecular Modeling Softwarewith Integrated Ruby Interpreter

Version 1.1.0

Toshi Nagata

Molby

å¯¾è©±ååå­ã¢ããªã³ã°ã½ããã¦ã§ã¢ï¼Ruby ã¤ã³ã¿ããªã¿å èµï¼

Version 0.5.5 build 20110721

Version 1.1.0

æ°¸ç°ãå¤®

2. Get the Software

3. Installation

3-2. Mac OS X

3-2. Mac OS X

4. Uninstallation

4-1. Microsoft Windows

4-2. Mac OS X

2. ã½ããã¦ã§ã¢ã®å ¥æ

3. ã¤ã³ã¹ãã¼ã«

3-1. Microsoft Windows

3-2. Mac OS X

3-2. Mac OS X

4. ã¢ã³ã¤ã³ã¹ãã¼ã«

4-1. Microsoft Windows

4-2. Mac OS X

2. License

2. ã©ã¤ã»ã³ã¹

2. Rotate the Molecule

2. åå­ãåè»¢ããã

3. Adding and Deleting Atoms

3. åå­ãè¿½å ããã»åé¤ãã

ç¬¬ä¸æ®µéï¼åå­ãç·¨éããï¼ã«ããã»ã³ãã¼ã»ãã¼ã¹ã

Step Four: Energy Minimization by Molecular Mechanics

Step Four: Ring Fusion

1. Ring fusion by double-click and type-in

2. Ring fusion by copy-and-paste

ç¬¬åæ®µéï¼ç¸®ç°æ§é ã®ä½æ

1. ããã«ã¯ãªãã¯ï¼ã­ã¼å ¥åã«ããç¸®ç°

2. ã³ãã¼ï¼ãã¼ã¹ãã«ããç¸®ç°

Step Five: Edit a Molecule: Using a Property Table

1. The Property Table of a Molecule

2. The Bond/Angle/Dihedral/Improper Table

3. The Parameter Table

ç¬¬äºæ®µéï¼åå­ãç·¨éããï¼å±æ§ãã¼ãã«ãä½¿ã

1. åå­ã®å±æ§ãã¼ãã«

2. Bond/Angle/Dihedral/Improper ãã¼ãã«

3. ãã©ã¡ã¼ã¿ãã¼ãã«

Step Six: Energy Minimization by Molecular Mechanics

1. About Molecular Mechanics Implementation in Molby

2. Energy Minimization How-to

2. Energy Minimization How-to

3. Handling electrostatic interaction

3. Handling electrostatic interaction

ç¬¬åæ®µéï¼åå­åå­¦è¨ç®ã«ããã¨ãã«ã®ã¼æå°å

ç¬¬å ­æ®µéï¼åå­åå­¦è¨ç®ã«ããã¨ãã«ã®ã¼æå°å

1. Molby ã®åå­åå­¦è¨ç®ã«ã¤ãã¦

2. ã¨ãã«ã®ã¼æå°åã®æ¹æ³

2. ã¨ãã«ã®ã¼æå°åã®æ¹æ³

3. éé»ç¸äºä½ç¨ã®åãæ±ã

3. éé»ç¸äºä½ç¨ã®åãæ±ã

Step Five: Edit a Molecule: Using a Property Table

1. The Property Table of a Molecule

Step Seven: Molecular Dynamics (MD) Calculation

1. MD Calculation within Molby

ç¬¬äºæ®µéï¼åå­ãç·¨éããï¼å±æ§ãã¼ãã«ãä½¿ã

Step Six: Collaboration with Other Quantum Chemistry Softwares

ç¬¬å ­æ®µéï¼ä»ã®éå­åå­¦ã½ããã¦ã§ã¢ã¨ã®é£æº

Step Seven: Using Embedded Ruby Interpreter

ç¬¬ä¸æ®µéï¼çµã¿è¾¼ã¿ Ruby ã¤ã³ã¿ããªã¿ãä½¿ã

Reference

ãªãã¡ã¬ã³ã¹

2. Using Molby with AMBER: Creating Inputs and Importing Outputs

3. Using Molby with NAMD: Creating Inputs and Importing Outputs

4. Building Solvated Structures

ç¬¬ä¸æ®µéï¼åå­ååå­¦è¨ç®

1. Molby çµã¿è¾¼ã¿ã®åå­ååå­¦ (MD) è¨ç®

2. AMBER ã¨ã¨ãã«ä½¿ãï¼å ¥åã®ä½æã¨åºåçµæã®ã¤ã³ãã¼ã

3. NAMD ã¨ã¨ãã«ä½¿ãï¼å ¥åã®ä½æã¨åºåçµæã®ã¤ã³ãã¼ã

4. æº¶åªåæ§é ã®ä½æ

An Interactive Molecular Modeling Software
with Integrated Ruby Interpreter

Interactive Molecular Modeling Software
with Integrated Ruby Interpreter

å¯¾è©±åååã¢ããªã³ã°ã½ããã¦ã§ã¢
ï¼Ruby ã¤ã³ã¿ããªã¿åèµï¼

æ°¸ç°ãå¤®

2. ã½ããã¦ã§ã¢ã®å¥æ

3. ã¤ã³ã¹ãã¼ã«

4. ã¢ã³ã¤ã³ã¹ãã¼ã«

2. ã©ã¤ã»ã³ã¹

2. ååãåè»¢ããã

3. ååãè¿½å ããã»åé¤ãã

ç¬¬ä¸æ®µéï¼ååãç·¨éããï¼ã«ããã»ã³ãã¼ã»ãã¼ã¹ã

ç¬¬åæ®µéï¼ç¸®ç°æ§é ã®ä½æ

1. ããã«ã¯ãªãã¯ï¼ãã¼å¥åã«ããç¸®ç°

2. ã³ãã¼ï¼ãã¼ã¹ãã«ããç¸®ç°

ç¬¬äºæ®µéï¼ååãç·¨éããï¼å±æ§ãã¼ãã«ãä½¿ã

1. ååã®å±æ§ãã¼ãã«

2. Bond/Angle/Dihedral/Improper ãã¼ãã«

3. ãã©ã¡ã¼ã¿ãã¼ãã«

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