[gmx-users] RNA

Yang Ye leafyoung81-group at yahoo.com
Tue Sep 20 17:06:02 CEST 2005

You need add entries into FF.dat.

If you would like to simulate NA, you may try out Folding at home's AMBER 
port. http://folding.stanford.edu/ffamber/
It has detailed steps of setup. You can learn it from there.

Yang Ye

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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