[gmx-users] RNA

[Maik Goette]

If I am not totally wrong, pdb2gmx should find it, if the path is set, 
and the files are copied into the topology dir.
Example:
pdb2gmx -f x.pdb -ff oplsaa

If this doesn't work, a fast solution is to put all the FF-files in the 
working directory.

For your 2. question:
Obviously the terminal ends of RNA are not included, yet.
So you have to insert them manually. If not, GROMACS will complain about 
  missing 5' atoms (P and 2x O), which shouldn't exist at the terminal 
end, but GROMACS awaits them, because no terminal "residues" are defined.
It also won't add the hydrogen to the 3' end.
If you aren't used to GROMACS and it's FF-files, it could be a hard job 
for you to fix/do that...but, you will learn a lot about GROMACS and its 
files, if you do...now it's up to you. ;)

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/


vincenzo venditti wrote:
> Yes, I am using the -ff option of pdb2gmx command
> 
> Regards
> 
>     ------------------------------------------------------------------------
>     From:  /Maik Goette <mgoette at mpi-bpc.mpg.de>/
>     Reply-To:  /Discussion list for GROMACS users <gmx-users at gromacs.org>/
>     To:  /Discussion list for GROMACS users <gmx-users at gromacs.org>/
>     Subject:  /Re: [gmx-users] RNA/
>     Date:  /Wed, 28 Sep 2005 12:30:40 +0200/
>      >Are you using the -ff flag ?
>      >
>      >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/
>      >
>      >
>      >vincenzo venditti wrote:
>      >>Dear All,
>      >>I'm trying to carried out a MD simulation on a short RNA molecule
>      >>(It's the first time that I work on such molecules). I've
>      >>downloaded the Force Field ffoplsaanr from the web page
>      >>http://rnp-group.genebee.msu.su/3d/oplsa_ff.html. Then I've copied
>      >>the new Force Field files in the GROMACS Force Fiel directory, but
>      >>when I run pdb2gmx command I'm not able to find the new Force
>      >>Field. How can I do?
>      >>  Another question: In the web page
>      >>_group.genebee.msu.su/3d/oplsa_ff.html_ I've found "Add records for
>      >>RNA 3' and 5' ends (for DNA it has already been added)". What does
>      >>it means?
>      >>  Thanks in advance,
>      >>Vincenzo
>      >>
>      >>------------------------------------------------------------------------
>      >>Condivi foto, pensieri ed altro ancora creando il tuo Blog su MSN
>      >>Spaces. E' gratis! <http://g.msn.com/8HMBITIT/2746??PS=47575>
>      >>
>      >>
>      >>------------------------------------------------------------------------
>      >>
>      >>_______________________________________________
>      >>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.
>      >_______________________________________________
>      >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.
> 
> 
> ------------------------------------------------------------------------
> Hai bisogno di una risposta immediata? Prova MSN Messenger. 
> <http://g.msn.com/8HMBITIT/2743??PS=47575>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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.