5. Structure Building

5.1. Modelling a single molecule

Select one of the following methods.

  • Open a various format file (PDB, mol, mol2, SDF, CIF, xyz etc.) at Open or drag and drop to the main window.

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

  • Draw a structural expression directly with Tools ‣ Enter a structural formula.

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

    Select the appropriate operations from Edit menu.

    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 the point charge on Winmostar, which is necessary for MD calculation.

When using the default AM1/BCC charge, it is not necessary to explicitly set charge. Also, for water molecules, the charge value of the selected water model is automatically applied.

If you want to use a charge other than AM1/BCC, create one molecule by the method Modelling a single molecule and then assign a charge by the following method. The allocated charges can be displayed and checked by modifying display ‣ Label/Charge.

  • Assign Gasteiger charge.

    Assigning a charge manually by MD ‣ Assign Charges Manually ‣ By Acpype. For ions, input the charge in Total charge [e]. If it is an ion, input the charge in Total charge [e].

  • Assign RESP charge.

    1. In QM ‣ GAMESS ‣ Preference ‣ Easy Setup, set the calculation method and the base function to “HF/6-31G*” and select ESP/RESP for Method. For ions, input the charge to Charge.
    2. Close the Easy Setup window with the OK button and press the:guilabel:Run button in the configure window to execute the calculation.
    3. When the GAMESS calculation is finished, retrieve the RESP charge at QM ‣ GAMESS ‣ 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 Charges (arc).
    • For Quantum ESPRESSO, use Solid ‣ Quantum ESPRESSO ‣ Lowdin Charge.
    • Otherwise, open the log file in the main window.
  • Enter values for each element.

    • Assigning a charge manually by MD ‣ Assign Charges Manually ‣ By Manual Entry.
  • Enter a value for the selected atom.

  • 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. In MD ‣ Create/Edit Cell, set the value of Create ‣ Distance and press the Create button. Adjust the size of the cell and press the OK button.

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 ‣ Save As in mol2 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 mol2 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

  • Since the system may fail at higher densities, start at a lower density (about 40 % of the experimental value if the experimental value is known) and gradually compress it to the desired density and pressure using constant pressure calculations.
  • Use Modify Selected Group ‣ Replicate Group, Create/Edit Cell and Append 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 (here we will call it a monomer) 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 monomer.

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

  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

  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. Set the value of Expand ‣ Width and Axis at Edit ‣ Create/Edit Cell and press the Expand button. Then, 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 ‣ Save As in mol2 format.
  3. Select MD ‣ Solvate/Build Cell.
  4. Decide which molecule and how many molecules to put in the other phase. In the case of a water molecule, click Add Water. Otherwise, click Add mol2 File to select a 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. Check Set Lattice Constants in Simulatoin Cell tab and click Same as main window button. Next, select “triclinic” at Box Type. The cell size of the first phase is shown to the right of Set Lattice Constants. In this case, change the value of the rightmost column (z-direction). In this case, refer to the density displayed on the right of Set Density above it.
  8. Press the Build button.
  9. Save a file by File ‣ Save As 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 ‣ Save As.
  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.

5.11. 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.
  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 ‣ Save As in 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 on File ‣ Append and select the mol2 file of the adsorbed molecule you just saved. Then, change the orientation and position of the adsorbed molecule using functions such as edit ‣ group edit ‣ Rotate Group Around Marked Atom , Rotate (Numerical) , Rotate by Aligning Marked Atoms , Move (Direct) , Move (Numerical) and so on.

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 ‣ Save As.
  3. Create the other solid using the method Creation of inorganic slabs (surfaces).
  4. Save the file as a cif from file ‣ Save As.
  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.