[gmx-users] RNA

[Alan Dodd]

Bear in mind that the leading ff on the forcefield
file name is not required in the option - I use the
command -ff gmx to use the file ffgmx.  Illogical, but
may help you.

--- vincenzo venditti <vincenzovenditti at hotmail.com>
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
>>
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