5. Structure Building

5.1. Modelling a single molecule

Select one of the following methods.

• Draw and read structure expressions with file ‣ import ‣ Structural Formula.

• Read SMILES format string from File ‣ Import ‣ SMILES.

• Load files in various formats (PDB, mol, mol2, SDF, CIF, xyz, etc.) by file ‣ Import File or drag and drop into the main window.

• Build 3D molecular structure from directly on the main window.

  Return to the initial structure with edit ‣ Reset Structure and select the required operation from Edit menu as appropriate.

  1. Execute Replace with Fragment to the initial structure (carbon and hydrogen atoms) so that the shape approaches a certain degree to the target molecule.

  2. For structures with adjacent aromatic rings, execute Build Ring.

  3. Execute Delete at the place where you want to delete the unnecessary substructure.

  4. In a place where you want to add a hydrogen atom, execute To marked atoms (Single), (Double), (Triple).

  5. Execute Element at the place where you want to change the element of atom.

  6. Execute Add/Change Bond where you want to create chemical bonds. Also change the type of binding by the same operation.

  7. Execute Quick Optimization to adjust to a reasonable atomic arrangement. (Only when the number of atoms is small)

  8. To explicitly rotate the substructure, execute Modify Selected Group ‣ Rotate Around Axis (2 Marked Atoms).

  9. For molecules that can take various conformations, Tools ‣ Conformation Search (Balloon) and choose a structure with low energy.

• In the case of a polymer, you can model a whole molecule directly, but it is more efficient to use the method of Creating polymer melt system.

5.2. Assigning point charges

I will show you how to set up the point charges required for MD calculations on Winmostar. First create a single molecule using the Modelling a single molecule method, then assign the charges using the following method. The assigned charges can be displayed and checked by changing Label/Charge.

Note that there is no need to explicitly set the charge for water molecules, since the water model charge values selected at the time of force field assignment are applied unconditionally.

If you want to average or shift the charge of some atoms, use Average the group’s charge or Shift Charges of Group.

• Assign Gasteiger charge.

  Assigning a charge manually by MD ‣ Assign Charges Manually ‣ Use AM1-BCC/Gasteiger charges. For ions, input the charge in Total charge [e]. If it is an ion, input the charge in Total charge [e].

• Assign RESP charge automatically.

  :Assigning charges by menuselection:MD –> manually assign charge –> Use RESP charges procedure. For ions, enter the charge in Total charge [e].

• Manually assign RESP charges in GAMESS or Gaussian.

  1. In file mode, at QM ‣ GAMESS/Gaussian ‣ Keyword Setup ‣ Easy Setup, set the calculation method and basis functions to “HF/6-31G*”, select Method Select :guilabel:`Method and ESP/RESP. For ions, enter the charge in Charge.

  2. Close the Easy Setup window with the OK button and press the Run button in the GAMESS/Gaussian Setup window to run the calculation

  3. When the GAMESS/Gaussian calculation is finished, get the RESP charge at QM ‣ GAMESS/Gaussian ‣ result analysis ‣ RESP Charges.

• Read the charge calculated from the population analysis, e.g. Mulliken or Lowdin charge, for into the main window.

  • In the case of MOPAC, read in the procedure of MO & Charges (mgf).

  • For Quantum ESPRESSO, use Solid ‣ Quantum ESPRESSO ‣ Lowdin Charge.

  • Otherwise, open the log file in the main window.

• Enter a value for the selected atom.

  • Group select atoms for which you want to input a charge in the Viewport, and then input a charge from Edit ‣ Change Atom Property ‣ Charge/Spin Density.

  • edit ‣ Edit Charge to enter charge from.

• Edit and assign directly on the text file.

  • Once the molecular structure is saved in File ‣ Save As in mol2 format, open the mol2 file with any text editor and edit the values in the ninth column of the section starting with @<TRIPOS>ATOM. After editing, click on file ‣ Reload to load the edited structure.

• In the case of polymers, the method of Creating polymer melt system is used because it takes time to calculate AM1/BCC and RESP charges of the whole molecule directly.

5.3. Creating an isolated system (gas phase)

1. Create a structure of one molecule (See Modelling a single molecule). In the case of quantum chemistry simulation, since the period boundary condition is not used, the subsequent operation is unnecessary.

2. In the case of MD simulation, assign point charges (See Assigning point charges).

3. Create a cell by Edit ‣ Create/Build Cell ‣ Create/Edit Cell.

5.4. Creating a small molecule liquid system

1. Create a structure of one molecule (See Modelling a single molecule).

2. In the case of MD simulation, assign point charges (See Assigning point charges).

3. Save a file by File ‣ Export File in mol2 or wmm format.

4. Procedures 1 to 3 are performed for all molecular species to be calculated.

5. Select MD ‣ Solvate/Build Cell.

6. Determine which molecules to put in the system. For the molecules displayed in the main window, press Add Displayed Molecule. For water molecules, press Add Water. For the other cases, press Add File.

7. Enter the number of molecules to be inserted into the system.

8. Perform 6 and 7 for all molecular species you want to calculate.

9. Set the system size at Simulation Cell and press Build button.

Note

• If the density is too high, the creation of the system may fail, so start with a low density (about 40 % of the experimental value of the substance of interest or a substance similar to the substance of interest, if known) and adjust the density with Edit ‣ Create/Edit cell ‣Transform Cell or run the MD calculation and compress gradually to the desired density and pressure with a constant pressure calculation.

• Use Modify Selected Group ‣ Replicate Group, Create/Edit Cell and Import File when CygwinWM is not installed or it is difficult to arrange with Solvate/Build Cell.

5.5. Creating polymer melt system

1. Create a polymer repetition unit to be calculated by the method Modelling a single molecule. For example, in the case of polyethylene, create an ethane molecule instead of an ethylene molecule.

2. In the case of MD calculation, the charge is assigned by the method Assigning point charges in the state of the repeting unit.

3. In Molecule Display Area, left-click two atoms connected with the neighboring repeat unit and register them as monomers by MD ‣ Polymer ‣ Register repeat unit.

4. Depending on the structure of the polymer to be created, perform operations MD ‣ Polymer ‣ Homo Polymer builder, Block Polymer Builder and Random Polymer Builder.

   Tip

   • For example, in the case of a structure like -[AAABBB]-, create AAABBB using Block Polymer Builder first, then open a wpo file generated in the wpo folder, register as a new repeat unit at Register repeat unit and execute Homo Polymer builder.

5. Create a simulation cell by performing the operation MD ‣ Polymer ‣ Polymer Cell Builder.

6. If a small molecule component is dissolved in the polymer, create the dissolved small molecule by the procedure of Modelling a single molecule and Assigning point charges and save it in mol2 format beforehand. Then, select and insert the mol2 file of small molecule at MD ‣ Insert Molecules, which was saved after step 5. If the density is not set low in step 5, the insertion of small molecule components may fail.

5.6. Creating gas-liquid interface

1. Create a liquid phase (see Creating a small molecule liquid system).

2. In Edit ‣ Transform Cell, check Transform only along the selected axis and Do not change, then check Set incremental length or Set total length, enter a value and press the OK button.

   Note

   • Select edit ‣ Wrap Around Cell Boundary before expanding the structure of the liquid phase because there are many atoms with coordinates outside the simulation cell in the structure after MD calculation. For molecular systems, select relocate molecular units inside the cell; for inorganic systems, select relocate atomic units inside the cell.

5.7. Creating gas-liquid interface

1. Create one of the liquid phases using Creating a small molecule liquid system. At this time, a mol2 file should be created in advance for all types of molecules contained in the two phases.

2. Save a file by File ‣ Export File in mol2 format.

3. Select MD ‣ Solvate/Build Cell.

4. Decide which and how many molecules to put in the other phase. For water molecules, click Add Water. Otherwise, click Add File and select the mol2 file.

5. Enter the number of molecules to be inserted into the system.

6. Perform the steps in 4 and 5 for all the molecular species you want to calculate.

7. On the Simulatoin Cell tab, check the Set Lattice Constants and click the Same as main window button. Next, select “triclinic” for the Box Type. To the right of the Set Lattice Constants, the cell size of the first phase you created is displayed. Click the Change only one direction, select Z with the Select direction, and enter the specified density with the Enter density to automatically set the lattice constants in the z and y directions while keeping the x and y constants fixed.

8. Press the Build button.

9. Save a file by File ‣ Export File in mol2 format.

10. Click MD ‣ Interface Builder.

11. Click Browse button of Cell 1 in the Cell tab, and select the file saved in step 2. Similarly, in Cell 2, select the file which was saved in 9.

12. Input the distance between liquid phases in Direction tab of Interval.

13. Click Build button, type the name of the file to save, and then click Save button.

5.8. Protein creation (no ligand)

1. Open the pdb file of the protein you want to calculate with Winmostar.

2. Use Select ‣ Select by Molecular Species to select a group of non-protein components (e.g., binding water, buffers, ligands, etc.), and then use Edit ‣ Modigy Selected Group ‣ Delete to delete the selected group.

3. Edit ‣ Add Hydrogen ‣ Using pdb2gmx. Even if hydrogen appears to be added before the execution, the calculation may fail later if this process is omitted.

4. Click MD ‣ Solvate/Build Cell. Click Add Displayed Molecule, type “1” in Enter # of molecules and click the OK button. Next, click Add Water button, input the number of molecules (about 5000 to 10000) at Enter # of molecules and click OK button. Then, click the Build button.

5. To neutralize the system, place ions with the procedure MD ‣ Generate Ions. If the message “WARNING: The charges defined on the main window will be discarded. Are you sure you want to continue?” is displayed, click Yes.

If the MD calculation is executed after the above procedure, it is desirable to continue the MD calculation after the above procedure because if the file is saved after the above procedure is executed, the residue information may not be saved properly.

5.9. Protein creation (with ligands)

1. Open the pdb file of the protein-ligand complex you want to calculate with Winmostar.

2. Use Select ‣ Select by Molecular Species to select a group of non-ligand components (proteins, bound water, buffers, etc.), and then use edit ‣ Delete to delete the selected group.

3. Execute Edit ‣ Add Hydrogens ‣ Using OpenBabel.

4. Save the structure of the ligand in mol2 format with file ‣ Export File.

5. Open the pdb file of the protein-ligand complex you want to calculate again with Winmostar.

6. Use Select ‣ Select by Molecular Species to select a group of non-protein components (e.g., binding water, buffers, ligands, etc.), and then use Edit ‣ Modigy Selected Group ‣ Delete to delete the selected group.

7. Edit ‣ Add Hydrogen ‣ Using pdb2gmx. Even if hydrogen appears to be added before the execution, the calculation may fail later if this process is omitted.

8. Click Solvate/Build Cell. Click Add Displayed Molecule, type “1” in Enter # of molecules and click the OK button. Next, click Add Water button, input an appropriate number of molecules at Enter # of molecules and click OK button. Then, click Add mol2 File button, open the mol2 file saved in step 4, type “1” in Enter # of molecules, and click OK button. Do you want to arrange these molecules in a random manner? If asked, click No. Then, click the Build button.

9. To neutralize the system, place ions with the procedure MD ‣ Generate Ions. If the message “WARNING: The charges defined on the main window will be discarded. Are you sure you want to continue?” is displayed, click Yes.

If the MD calculation is executed after the above procedure, it is desirable to continue the MD calculation after the above procedure because if the file is saved after the above procedure is executed, the residue information may not be saved properly.

5.10. Preparation of inorganic crystals

If you already have the crystal data you want to calculate, such as a CIF file, open the file with Winmostar. If such a file does not exist, perform the following operations.

1. Click on solid ‣ Crystal Builder.

2. Select the following item at the top right of Crystal Builder window.

   • Select the classification of a crystal from Crystal System of Lattice.

   • Select a space group of a crystal from Space Group of Lattice. The choices of Space Group are changed by Crystal System.

   • In Lattice Constants, input the lattice constants of the crystal to be computed.

3. Crystal Builder Input an atom of an asymmetric element in the list at the bottom right of the window.

   • Double-click on the Atom field and enter the type of element.

   • Double-click the fields of X , Y , Z to fill in the coordinates.

   • Add an atom by Add button.

   • Removes a selected atom by clicking Remove button.

4. Click the OK button to apply the structure specified by the crystal builder to the main window.

5. Use Edit ‣ Create/Edit Cell ‣ Transform Cell if you want to apply a strain to a crystal.

5.11. Preparation of inorganic crystals (with point defects or elemental substitutions)

1. Open a CIF file of the crystal with no defects or create a crystal structure with the method Preparation of inorganic crystals.

2. Click on Solid ‣ Generate Supercell. Increase the value of a , b , c and specify the size of the supercell (first, about 2 in each direction). Finally, click the OK button.

3. In the main window, left-click on the atom you want to create a point defect, or the atom you want to replace the element with, and a red marker will appear.

4. To create a point defect, click Edit ‣ Delete atom.

5. To replace an element, select the element from Edit ‣ Select Element for Editing Ops and then click on Edit ‣ Change Atom Property ‣ Element.

5.12. Creation of inorganic slabs (surfaces)

1. Open a CIF file of the crystal in bulk, or create a crystal structure with Preparation of inorganic crystals.

2. Click on solid ‣ Build Cluster Model.

3. Enter the items above Generate Slab button, Miller indices (h k l) etc., then click the Generate Slab button.

4. Click the Generate Slab button after enteringthe following items below Generate Slab button. If the atomic configuration of both the front and back of the slab structure you want to create is not among the choices of Surface configurations, ensure that the atomic arrangement on at least one side is the desired structure, then click OK and delete an unwanted atomic layer with Delete function in the main window. To make the atomic layer thicker in advance, increase the value of Minimum slab size above Generate Slab button .

5.13. Creation of molecular adsorption surfaces

1. Create a molecule to be adsorbed by the method Modelling a single molecule.

2. Save a file by File ‣ Export File in wmm or mol2 format.

3. Create a surface with the method Creation of inorganic slabs (surfaces).

4. If necessary, click on solid ‣ Generate Supercell. Increase the value of a , b and specify the size of the supercell. Finally, click the OK button.

5. Click (mark) the atom directly below the position on the slab surface where you want the molecule to be adsorbed, then click Edit ‣ Add Atom ‣ Adding dummy atoms to the center of gravity of a group.Set the Axis to z, set the Distance appropriately, and click OK.

6. Click MD ‣ Replace Molecules Species=(unknown) and click OK. Then open the file exported in step 2.

7. If you want to rotate adsorbed molecules, use Edit ‣ Modify Selected Group ‣ Rotate by Aligning Marked Atoms or Rotate (Numerical). If you want to translate the adsorbed molecules, use Edit ‣ Modify Selected Group ‣ Move (Numerical). For example, if you want to adjust the distance between the surface first layer and a specific atom in an adsorbed molecule, first click the atom in the surface first layer, then click the specific atom in the adsorbed molecule, then Ctrl+click the adsorbed molecule to select the group. Then click Edit ‣ Edit Group ‣ Move (Numerical), change Definition to Relative coordinate between marked atoms and change the value of Z.

5.14. Creation of solid interfaces (grain boundaries)

1. Create one solid using the method Creation of inorganic slabs (surfaces).

2. Save the file as a cif from file ‣ Export File.

3. Create the other solid using the method Creation of inorganic slabs (surfaces).

4. Save the file as a cif from file ‣ Export File.

5. Click MD ‣ Interface Builder.

6. Click Browse button of Cell 1 in the Cell tab, and select the file saved in step 3. Similarly, in Cell 2, select a file which was saved in step 5.

7. Enter the distance between solids in Interval on Direction tab. Then check Specify interval on selected axis between outermost atoms of Interval

8. If you move to the Repeat tab, the top two (a-axis and b-axis) of the three Suggest buttons can be pressed. Click the Suggest button, select a row whose value of Ratio is close to 1 and the system size is not too large, and click the Set button.

9. Click Build button, type the name of the file to save, and then click Save button.

10. Select one of the solids as a group by Ctrl+Left dragging. See Select menu for details.

11. Click edit ‣ group editing ‣ Move (Numerical) to move the group in the X and Y direction. If you enable view ‣ Show Multi-View, it is easier to see the position.

5.15. Creating Molecular Crystals

At present, Winmostar does not have the ability to generate stable structures of physicochemically valid molecular crystals from the structure of a single molecule, so it is necessary to use a structure file of a molecular crystal obtained from a database or other source as a starting point. In such a structure file, the coordinates of molecules across the boundaries of the simulation cell are far apart, and the process will fail if such a structure file is directly used to perform force field assignment for molecular dynamics calculations such as Gromacs and LAMMPS. In this section, we introduce a processing method to prevent the force field assignment from failing as follows. Note that the following processing is not necessary when only first-principles calculations such as Quantum ESPRESSO and OpenMX are performed.

1. Draw and read structure expressions with file ‣ import ‣ Structural Formula.

2. Edit ‣ Wrap Around Cell Boundary and check Wrap for each atom and click OK.