[gmx-users] creating an rtp file

[Maik Goette]

Hi

Why do you want to create an rtp-file?
Which FF do you want to use?
For DNA I recommend AMBERFF (cause everyone does :) ), but
the group around Andrey Golovin did an implementation of DNA parameters 
into OPLS recently, which can be found here:
http://rnp-group.genebee.msu.su/3d/oplsa_ff.html

It's still under development and testing, but it seems to work.
The number of DNA-atoms doesn't really matter. just do a pdb2gmx with 
the right FF (which includes an rtp-file) and you'll receive a topology 
to work with.

Regards


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Gireesh M Krishnan wrote:
> I'm very new in using GROMACS. Can someone suggest me
> how to write a rtp file for a DNA strand which having
> about 700 atoms? any package available for such large
> systems?
> 
> regards,
> Gireesh 
> 
> ________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
> .
>