[gmx-users] gen pairs missing from vmd top
jalemkul at vt.edu
Sat May 10 02:16:00 CEST 2014
On 5/9/14, 7:35 PM, gromacs query wrote:
> Hi All
> I am using topo writegmxtop output.top in VMD and it writes fake sort of
> top file which needs further user based adjustments.
> The top file so generated has all [bonds] [angles] [dihedral] information
> but [pairs] are missing. I am using charmm36 which says gen-pair =yes in
> forcefield.itp. Does this mean it won't matter if I include or not [pairs]
> information in top file?
> pdb2gmx does explicitly prints [pairs] information when I generate top file
> for some default residues in rtp file.
> So should I mention them explicitly? Is there any script/command which can
> generate them as I have bond information (one can write own script simply
> if its a linear molecule but branching makes thing difficult).
Pairs do need to be listed explicitly in the .top file. The gen-pairs keyword
only affects the generation of pairtypes; if set to "yes" it will use normal
combination rules for any pair that does not have [pairtypes] explicitly listed
in ffbonded.itp (which, in the case of CHARMM, is all of them).
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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