[gmx-users] Regarding topology generation by using topologen_1.1.pl script

Dilip H N cy16f01.dilip at nitk.edu.in
Tue Oct 24 19:11:09 CEST 2017

I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
topology. But the net charge on the molecule is 0.18 (for one molecule of

1] So how do i neutralize the net charge (because it is difficult to add a
non-integer charge), and hence carry out the simulation as neutral

2] Or is it possible to run by other scripts like mktop, acpype etc..??

Any suggestions are appreciated.

With Best Regards,

Ph.D Student

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