[gmx-users] gen pairs missing from vmd top

Justin Lemkul 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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