6.13 Missing parameter table

VEGA ZZ shows this table when a molecular mechanics calculation is starting (e.g. AMMP minimization) or a force field parameter check is requested (e.g. saving a molecule) and one or more parameters are missing in the current parameter file:


Missing parameter table


Each missing parameter occupies a line in the table that is subdivided in six columns: the first two columns have always the same meaning (Parameter and Atom type), and the other columns change the meaning on the basis of the parameter type (e.g. angle, bond, torsion, etc.) as reported in the following table:

Parameter type Column 3 Column 4 Column 5 Column 6
Angle Ktheta
Force constant, kcal/mol/rad2
Angle value, degrees
Urey-Bradley force constant, kcal/mol/2 (not used by AMMP)
1-3 distance, (not used by AMMP)
Bond Kb
Force constant, kcal/mol/2
Bond length,
- -
Torsion (dihedral) Kchi
Force constant, kcal/mol
Torsion offset, degrees
Hybrid (improper, out of plane) Kpsi
Force constant, kcal/mol/rad2
Hybrid offset, degrees
Nbond (non-bond) eps
epsilon, kcal/mol
half distance,
eps 1-4
epsilon 1-4, kcal/mol (not used by AMMP)
Rmin/2 1-4
half distance 1-4, (not used by AMMP)

Moving the cursor and clicking over the cells, the missing parameter is highlighted in the structure:


Highlight example


This is a picture example resulting by the click on the CT3-SE bond missing parameter cell. This behaviour can be changed un/checking the Color atoms, Labels and Wireframe items in the View menu: the first one allows to color the highlighted structure in red and the other atoms in white, the second one shows the atom type labels and the third one change the view to wireframe.
You can type the parameters selecting each cell, but if you don't have any idea about those values, the context menu can suggest them for you, clicking the cell with the right mouse button.
Another way to fix the parameters is the use of the automatic assignment. This function is accessible selecting Edit Auto assign in the menu bar. The method is a little bit dirty, but it's a good starting point to refine the missing parameters.
The new parameters can be saved in CHARMM format (*.inp) selecting File Save As ... menu item. In this way, you can merge the parameters with the user parameter file in the VEGA ZZ\Data\Parameters directory, in order to avoid to repeat the same operation for similar molecules (see InpMerge utility). You can use them with NAMD also:

# This is a simple NAMD 2 configuration file
# to perform an energy minimization

numsteps                8000
minimization            on
dielectric              1.0
coordinates             molecule.pdb
outputname              molecule
outputEnergies          1000
binaryoutput            no
DCDFreq                 1000
restartFreq             1000
structure               molecule.psf
paraTypeCharmm          on
parameters              par_all22_prot.inp
parameters              molecule.inp
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              8.0
cutoff                  12.0
pairlistdist            13.5
margin                  0.0
stepspercycle           20

The red line indicates the file with the parameters not included in the standard par_all22_prot.inp file and previously generated saving the missing parameter table. The PDB and the PSF files (blue) can be generated by VEGA ZZ using the save molecule function.

Clicking Ok button or selecting File Continue menu item, the procedure invoking the missing parameter table continues using the parameters edited by the user. Clicking Cancel button or selecting File Cancel menu item, the procedure is aborted.