[gmx-users] RNA

[Maik Goette]

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
> 
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