[gmx-users] Nucleic Acid Simulations with Gromacs

gigo at poczta.ibb.waw.pl gigo at poczta.ibb.waw.pl
Tue Oct 2 12:58:00 CEST 2007

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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list