[gmx-users] CMAP missing for a new residue.

Justin Lemkul jalemkul at vt.edu
Thu Sep 3 14:06:17 CEST 2015

On 9/3/15 3:42 AM, Dawid das wrote:
> Dear Gromacs Experts,
> I am working with fluorescent protein, posesing a chromophore which I
> defined as a non-standard " amino-acid residue". Now, I want to use
> Charmm22 force field and the issue is that I am missing CMAP parameters and
> these are not available in the literature.

FYI, CHARMM22 has no CMAP.  CHARMM22/CMAP (what GROMACS somewhat misleadingly 
calls "charmm27.ff") does.

> My question is, whether there is a way to use CMAP parameters only for
> connection between standard a.a. and omit them for connection between my
> chromophore and standard a.a.?

You'd probably have to modify the topology after the fact, but the connection 
between the chromophore and the next residue is easily omitted by not having a 
[cmap] directive in the chromophore .rtp file.  If the backbone of the 
chromophore has standard amino acid atom names, there's no way to tell pdb2gmx 
to not write a CMAP entry from the previous residue.  You can comment out or 
remove that line later.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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