[gmx-users] modelling a new molecule in OPLS

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 20 15:20:37 CEST 2008

When asking for free help, it is often best to make life easy on those 
from whom you're requesting it :-)   I don't know if anyone on this list 
is going to take the time to hunt through hundreds of lines of your 
topology, identify the atom numbers involved in your errors, determine 
which atoms those numbers correspond to, and try to figure out what your 
problem is.

That said, there is some general advice that I will give.  If grompp 
cannot find default parameters for a given set of atoms (for any item - 
bonds, angles, dihedrals, etc.) it is because they are not present in 
the original force field.  That means you either made a mistake in 
defining atom types or the numbering of the topology, or you will have 
to come up with the parameters for that item yourself.


> I have built an all atom topology file for "chaps" as i have already
> discussed in previous mails, with charges from Gaussian DFT. The current
> problem is with the grompp.
> The error results that:
> processing topology...
> Generated 342378 of the 342378 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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