[gmx-users] question

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 7 09:21:04 CEST 2015


You need to make sure you understand the parameterization philosophy of
your force field - so check out its original literature. You likely want to
be consistent. Hint, I suspect you won't find "we got stuff from Gaussian"
anywhere for GROMOS. Then look at the approaches others have taken to
develop ligands for such force fields for binding studies. You might find
http://compbio.biosci.uq.edu.au/atb/ useful


On Tue, Jul 7, 2015 at 6:23 AM Atila Petrosian <atila.petrosian at gmail.com>

> 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,
> Atila
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