19. How-to guide

This section includes some tricks to solve common problems with VEGA ZZ.

 

19.1 MEP calculation with semi-empirical charges
19.2 Volume calculation
19.3 Trajectory format conversion
19.4 Join two or more trajectory files
19.5 Remove the waters in the trajectory file
19.6 Add the side chains to a homology-modelled protein
19.7 AMMP energy minimization
19.8 Installation of Accelrys CHARMM force field
19.9 Conversion of a database to another format
 

19.1 MEP calculation with semi-empirical charges

  1. Open the molecule (File -> Open).
  2. Perform a single point Mopac calculation (Calculate -> Mopac): choose the calculation mode (AM1, MINDO/3, NMDO, PM3), check the total charge, add 1SCF in the Other field and click the Run button.
  3. Open the Surface calculation dialog box (Calculate -> Surface).
  4. Select MEP in the Type field.
  5. Choose the surface type (Dots, Mesh, Solid).
  6. Go to the Gradient tab, click with the right mouse button over the rainbow and select Preset -> MEP MLP.
  7. Return to the New tab, check Color by gradient and click the Calculate button.
  8. Please remember the best way to save the molecule with its surfaces is the use of the IFF file format.

 

19.2 Volume calculation

  1. Open the molecule (File -> Open).
  2. In the main menu select View -> Information.
  3. Press the Calculate button and ignore the possible warning messages about the logP calculation.
  4. Find the volume value in the output box.

 

19.3 Trajectory format conversion

  1. Open the trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix in the file name (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File -> Open); 2) Open the trajectory file (Calculate -> Analysis and thus click the open button in the dialog window).
  2. Save the trajectory (File -> Save trajectory), choosing the new file format.
  3. If you want save more disk space, you could save the trajectory in the Gromacs XTC format that uses the XDRF compression algorithm for the floating point data.

 

19.4 Join two or more trajectory files

  1. Make a copy of the first trajectory file.
  2. Open the second trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix in the file name (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File -> Open); 2) Open the trajectory file (Calculate -> Analysis and thus click the open button in the dialog window).
  3. Save the trajectory (File -> Save trajectory), using the format, the path and the file name of the first trajectory file. A requester will be shown: click Append. The trajectory will be joined to the end of the first one.
  4. Repeat the operation for each trajectory that you want join.

 

19.5 Remove the waters in the trajectory file

  1. Open the trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix in the file name (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File -> Open); 2) Open the trajectory file (Calculate -> Analysis and thus click the open button in the dialog window).
  2. Select the whole molecule without waters (Select -> No water).
  3. Save the new trajectory (File -> Save trajectory) checking Active only in the Options box.
  4. To open the new trajectory, you need an appropriate coordinate file without water molecules. To do it, remove the invisible atoms (Edit -> Remove -> Invisible atoms) and save the molecule with the same name of the new trajectory file (File -> Save As...).

 

19.6 Add the side chains to a homology-modelled protein

  1. Open the backbone file obtained by homology modelling (File -> Open).
  2. Add the side chains (Edit -> Add -> Side chains).
  3. Check the ring intersections (Calculate -> Protein check -> Ring inter.).
  4. If one or more ring intersections are found, you must fix them, rotating the Chi1 torsion (Edit -> Change -> Angle/torsion). At the end, repeat the ring intersection check.
  5. Add the hydrogens (Edit -> Add -> Hydrogens), selecting Protein as Molecule type, Residue end as Position of hydrogens and checking Use IUPAC atom nomenclature.
  6. Fix the atom types and the charges (Calculate -> Charges & pot.). Check if the total charge is correct.
  7. Save the molecule (File -> Save As ...). The IFF file format is strongly recommended.

 

19.7 AMMP energy minimization

  1. Open the molecule to minimize (File -> Open).
  2. Check the bond types. If they aren't correctly assigned, change them using Edit -> Change -> Bonds -> Find the bond types and finally click the Apply button. It's also possible to change manually the bonds using the Change bonds dialog (Edit -> Change -> Bonds).
  3. Assign the atom charges (Calculate -> Charge & Pot.). If you want, is possible to assign the SP4 potential in order to check if all atoms are correctly recognized. This is an optional step because AMMP fix automatically the potential if it's not already assigned.
  4. Open the AMMP dialog window (Calculate -> Ammp), select the minimization algorithm (e.g. conjugate gradients), the minimization steps (e.g. 3000), the toler value (e.g. 0.01), the number of steepest descent steps (e.g. 0).
  5. Click the Run button.

 

19.8 Installation of Accelrys CHARMM force field

The Accelrys CHARMM 22 force field allows to do MM/MD calculations of both small and big molecules with less problems than the standard CHARMM force field, because it was expanded with more atom types. For obvious copyright reasons, the ATDL template only (CHARMM.tem) is included in the VEGA ZZ package and not the parameter file (parm.prm), but if you have got an Accelrys software that includes the CHARMm license, you can use it, following this installation procedure:

  1. Copy the parm.prm file to ...\VEGA ZZ\Data\Parameters directory.
  2. To use it in a NAMD or AMMP calculation, when you fix the potentials (Calculate -> Charge & Pot.), select CHARMM (not CHARMM22_LIG, CHARMM22_LIPID, CHARMM22_NA and CHARMM22_PROT).

 

19.9 Conversion of a database to another format

If you want convert a database to another format, you need to create a new empty database in the desired format:

  1. Select File -> Database -> Open in the main menu.
  2. Choose the destination directory in which the new database will be created.
  3. Type the database name in the File name field.
  4. In the New database box, select the desired format.
  5. Click Create. The new database will be created in the specified directory.
  6. Finally click the database name in the file list and press the Open button. The Database explorer window will be shown.
  7. Open the database to convert (use the Open button in the Database box).
  8. In the Database box, drag & drop the opened database to the empty database. All molecules will be copied from the old database to the new one. If you want stop the copy, click the Abort button close to the progress bar in the main window.