19. How-to guide

This section includes some tricks to solve common problems by 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 trajectory files
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, check 1SCF and click Run button.
3. Open the Surface calculation dialog box (Calculate Surface).
4. Select MEP in Type field.
5. Choose the surface type (Dots, Mesh, Solid).
6. Go to Gradient tab, click the rainbow by the right mouse button and select Preset MEP MLP.
7. Return to New tab, check Color by gradient and click Calculate button.
8. Remember that 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 main menu, select View Information.
3. Press 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 file name of the associated molecule doesn't have the same prefix  (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 file format that you need.
3. If you want to save more disk space, you could choose Gromacs XTC as trajectory format, because it 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 file name of the associated molecule doesn't have the same prefix  (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 format, path and 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 trajectory files

1. Open the trajectory file (File Open). If the file name of the associated molecule doesn't have the same prefix  (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 make 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 ...). 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 Apply. It's also possible to change manually the bonds by Change bonds dialog (Edit Change Bonds) or by context menu.
3. Assign the atom charges (Calculate Charge & Pot.). If you want, it's possible to assign the SP4 potential in order to check if all atoms are correctly recognized. This step is optional, because AMMP fixes 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 to 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 Open button in Database box).
8. In 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 Abort button close to the progress bar of the main window.