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

Dawid das addiw7 at googlemail.com
Fri Sep 4 10:52:24 CEST 2015

2015-09-03 13:06 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

> FYI, CHARMM22 has no CMAP.  CHARMM22/CMAP (what GROMACS somewhat
> misleadingly calls "charmm27.ff") does.
Yes, I was aware of that, just forgot to write CHARM22/CMAP.

> 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.

Well, to be honest I defined my chromophore residue (let's call it CH6) in
aminoacids.rtp file along with all other amino acids but in fact I do not
use [cmap] directive under CH6 definition. I use only [atoms], [bonds],
[angles], [dihedrals] and [impropers] directives.

Only the C and N atoms have standard amino acid atom names, because I did
not know how to define the proper connection between CH6 and natural amino
acids the other way around.
I will try to find those lines and comment them out.

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