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
 

19.1 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.