[gmx-users] gen pairs missing from vmd top

gromacs query gromacsquery at gmail.com
Sat May 10 01:35:09 CEST 2014

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).


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