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8. How-to guideThis section includes some tricks to solve common problems with VEGA ZZ.
18.1 MEP calculation with semi-empirical charges
18.2 Volume calculation
18.3 NAMD file preparation
18.4 Fixing the backbone in a NAMD simulation
18.5 Trajectory format conversion
18.6 Join two or more trajectory files
18.7 Remove the waters in the trajectory file
18.8 Add the side chains to a homology-modelled protein
18.9 AMMP energy minimization
18.10 Building molecules with ISIS/Draw
18.1 MEP calculation with semi-empirical charges
Open the molecule (File -> Open).
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.
Open the Surface calculation dialog box (Calculate -> Surface).
Select MEP in the Type field.
Choose the surface type (Dots, Mesh, Solid).
Go to the Gradient tab, click with the right mouse button over the rainbow and select Preset -> MEP MLP.
Return to the New tab, check Color by gradient and click the Calculate button.
Please remember the best way to save the molecule with its surfaces is the use of the IFF file format.
Open the molecule (File -> Open).
In the main menu select View -> Information.
Press the Calculate button and ignore the possible warning messages about the logP calculation.
Find the volume value in the output box.
Open the molecule to simulate with NAMD (File -> Open or drag & drop over the main window).
Assign the atomic charges and the atom types (Calculate -> Charges & pot.). Please take care of the potential type: you must use the same force field that you intend to use during the simulation. If your molecule has better atomic charges (e.g. semi-empirical or quantum mechanical), don't assign the Gasteiger- Marsili charges.
Save the molecule two times (File -> Save As...): the first one in PDB 2.2 format (the connectivity isn't necessary) and the second one in PSF X-Plor format.
18.4 Fixing the backbone in a NAMD simulation
Open the molecule to simulate with NAMD (File -> Open or drag & drop over the main window).
Select in the main menu: Edit -> Coordinates -> Constraints.
Select Fix in the Mode box, and Protein backbone in the Select box.
Click the Apply button: the fixed atoms (the backbone) will be coloured in blue.
Close the dialog and save the molecule (File -> Save
As...) in PDB 2.2 format checking Constraints in the Option
box. Please remember to add the following lines in the NAMD simulation file:
fixedAtoms on
fixedAtomsCol B
18.5 Trajectory format conversion
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).
Save the trajectory (File -> Save trajectory), choosing the new file format.
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.
18.6 Join two or more trajectory files
Make a copy of the first trajectory file.
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).
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.
Repeat the operation for each trajectory that you want join.
18.7 Remove the waters in the trajectory file
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).
Select the whole molecule without waters (Select -> No water).
Save the new trajectory (File -> Save trajectory) checking Active only in the Options box.
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...).
18.8 Add the side chains to a homology-modelled protein
Open the backbone file obtained by homology modelling (File -> Open).
Add the side chains (Edit -> Add -> Side chains).
Check the ring intersections (Calculate -> Protein check -> Ring inter.).
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.
Add the hydrogens (Edit -> Add -> Hydrogens), selecting Protein as Molecule type, Residue end as Position of hydrogens and checking Use IUPAC atom nomenclature.
Fix the atom types and the charges (Calculate -> Charges & pot.). Check if the total charge is correct.
Save the molecule (File -> Save As ...). The IFF file format is strongly recommended.
Open the molecule to minimize (File -> Open).
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).
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.
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).
Click the Run button.
18.10 Building molecules with ISIS/Draw
Edit your 2D molecule with ISIS/Draw. ISIS/Draw is free available for non-profit use at www.mdli.com.
Select the molecule (e.g. Edit -> Select All).
Export the molecule in MDL Mol format (File -> Export -> Molfile ...).
Open the exported 2D molecule with VEGA ZZ.
Add the hydrogens using the bond order method (Edit -> Add -> Hydrogens).
Fix the atom types and the charges (Calculate -> Charges & pot.), choosing SP4 and Gasteiger.
Perform an energy minimization with Ammp (Calculate -> Ammp), using conjugate gradients and toler = 0.01.
Warning: please check the bond order because it's used by Ammp to calculate the bond length. The aromatic rings must be aromatized with partial double bonds and not with single/double alternated bonds as in ISIS/Draw. To fix the problem, you could recalculate the bond order using Edit -> Change -> Bonds -> Find the bond types in VEGA ZZ.