[gmx-users] creating an rtp file

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Feb 24 10:49:57 CET 2005


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:

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.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.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 
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