[gmx-users] question

Atila Petrosian atila.petrosian at gmail.com
Tue Jul 7 06:23:25 CEST 2015

Dear gromacs users

I am doing md simulation of protein-ligand using 5.0 version of gromacs. I
want to use prodrg server for my ligand.

Based on Justin's opinion, the charges should be modified. The structure of
my ligand is in a way that I can't use charge of the functional groups
being in aminoacids or nucleic acids in gromos force fields.

I am going to obtain the charges from gaussian software. But I don't know
how to set charge groups and charge group numbers to satisfy gromos force
field (we have to keep groups of atoms with total charge 0 together)

Please guide me about this.

Best wishes,

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