On 8/27/14, 11:41 AM, Xiang Ning wrote:
Dear Justin,
Sorry I missed the reply for yesterday. So the atoms are mostly from my peptide:
319: atom C of VAL, 321: N of ILE, 323: CA of ILE, 338, C of ILE, and one from
lipid POPC: 341: atom N of POPC. I just used "pdb2gmx -f box.gro -p box.top" to
obtain the top file of the whole system, which including water, protein, lipid
and ions. It generated several itp file and one top file. The CMAP is in
"box_Protein.itp", which included the itp file of protein and lipid. After that,
I ran grompp, and then the problem "unknown cmap torsion" occurred. I think the
torsion was because it can not tell apart the last peptide atom and the first
lipid atom. Could you please let me know how to solve this problem? Thanks a
lot!
This is indeed a result of asking pdb2gmx to process the heterogeneous
environment. Unfortunately, the lipid atom name is N, and since there are
bonded interactions in amino acids with +N atoms (i.e. the next residue), you're
probably going to get a lot of spurious bonded interactions (not just CMAP).
Your options:
1. Separate the components of the system (protein and lipids) for processing by
pdb2gmx. Processing a single lipid to get a .top that you can convert to .itp
is my preferred method.
2. Manually remove the spurious interactions from the existing .top file. There
will probably be a lot.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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