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.
-Justin
ANINDITA GAYEN wrote:
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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