[gmx-users] Re: DNA-ligand interactions with AMBER

Alan alanwilter at gmail.com
Wed May 13 09:15:01 CEST 2009

Please, take a look at acpypi.googlecode.com. I hope it can help you.


On Wed, May 13, 2009 at 06:12,  <gmx-users-request at gromacs.org> wrote:

> Subject: [gmx-users] DNA-ligand interactions with AMBER
> Dear Gromacs users
> I am simulating the interactions between ligands and DNA
> using GROMACS with the AMBER force field, as implemented with
> the AMBER PORT for GROMACS. Simulating DNA is actually
> very easy with this protocol, but for the ligand some
> problems arise. Until now we are constructing the
> topology manually, but this became complicated for large
> ligands. What is the best way to construct ligand
> topologies with AMBER parameters, for using with GROMACS,
> provided that we DO NOT have the AMBER package?
> Thank you very much in advance.
> Paulo Netz
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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