Grange Hermitage wrote:
Hi all,
What approach to use to generate a topology file for peptides which
include artificial residues such as serine with its sidechain extended
by two carbons to double bond with another such residue i.e.
CA-CB-OG-C1-C3=C4-C2-OG-CB-CA
Also I need to generate a topology for another type of
artificial peptide which includes beta-3 residues (C inserted in
mainchain between CA and C ).
Say I want to use a force field other than the 2 supported by the
PRODRG2.5 server.
I have tried to defining ff*.rtp residue definitions, but .top generated
by pdb2top are missing defaults essential for grompp (gb_ gd_). The
residue definitions have only [ atom ] specifications, allowing
the other sections to default as per the manual.
Well, then the defaults don't apply for whatever you've tried to connect.
Basically, check out the *bon.itp file for your force field and make sure the
parameters that you think you are generating are actually there, and then check
the naming you've given your atom types to make sure it is appropriate and
compatible with the ones that the force field is expecting.
Without showing us what you've tried, it's difficult to diagnose.
-Justin
thanks,
Grange.
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--
========================================
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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