[gmx-users] CMAP missing for a new residue.
addiw7 at googlemail.com
Fri Sep 4 12:17:32 CEST 2015
It seems to work :). Thank you!
2015-09-04 9:52 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
> 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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