[gmx-users] Nucleic Acid Simulations with Gromacs

[gigo at poczta.ibb.waw.pl]

Hi,
On the gromacs webpage in user contributions->topologies you have (at 
least) 2 forcefields do download that allow you to simulate NA. The first 
is OPLS NA records from rnp-group
(http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 
3.2.1, so minor manual adjustments for 3.3.1 are required. The second is 
AMBER ff variants from Stanford (http://folding.stanford.edu/ffamber/).
Good Luck


Grzegorz Wieczorek
Department of Bioinformatics
Institute of Biochemistry and Biophysics
Polish Academy of Sciences
ul. Pawinskiego 5a
02-106 Warszawa, Poland

On Tue, 2 Oct 2007, Monika Sharma wrote:

> Dear All,
> I want to start nucleic acid simulations. I am using gromacs3.3.1. But I 
> could not find any mention of Nucleic Acids in any of the force-field 
> provided by gromacs distro. So does it mean that one _can not_ simulate 
> nucleic acids with gromacs. Has anyone tried? And if someone can guide me 
> through??
> Thanks in advance
> Regards,
> Monika
>
>
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