[gmx-users] Unknown cmap torsion between atoms

Justin Lemkul jalemkul at vt.edu
Wed Aug 27 17:54:06 CEST 2014

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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