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

Paulo Netz paulo.netz at gmail.com
Wed May 13 18:23:43 CEST 2009

Thank you very much!

Paulo Netz

On 5/13/09, Alan <alanwilter at gmail.com> wrote:
> Please, take a look at acpypi.googlecode.com. I hope it can help you.
> Alan
> 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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