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<P>Yes, I am using the -ff option of pdb2gmx command</P>
<P>Regards<BR><BR></P></DIV>
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<DIV></DIV>From: <I>Maik Goette <mgoette@mpi-bpc.mpg.de></I><BR>Reply-To: <I>Discussion list for GROMACS users <gmx-users@gromacs.org></I><BR>To: <I>Discussion list for GROMACS users <gmx-users@gromacs.org></I><BR>Subject: <I>Re: [gmx-users] RNA</I><BR>Date: <I>Wed, 28 Sep 2005 12:30:40 +0200</I><BR>>Are you using the -ff flag ?<BR>><BR>>regards<BR>><BR>>Maik Goette, Dipl. Biol.<BR>>Max Planck Institute for Biophysical Chemistry<BR>>Theoretical & computational biophysics department<BR>>Am Fassberg 11<BR>>37077 Goettingen<BR>>Germany<BR>>Tel. : ++49 551 201 2310<BR>>Fax : ++49 551 201 2302<BR>>Email : mgoette[at]mpi-bpc.mpg.de<BR>> mgoette2[at]gwdg.de<BR>>WWW :
http://www.mpibpc.gwdg.de/groups/grubmueller/<BR>><BR>><BR>>vincenzo venditti wrote:<BR>>>Dear All,<BR>>>I'm trying to carried out a MD simulation on a short RNA molecule <BR>>>(It's the first time that I work on such molecules). I've <BR>>>downloaded the Force Field ffoplsaanr from the web page <BR>>>http://rnp-group.genebee.msu.su/3d/oplsa_ff.html. Then I've copied <BR>>>the new Force Field files in the GROMACS Force Fiel directory, but <BR>>>when I run pdb2gmx command I'm not able to find the new Force <BR>>>Field. How can I do?<BR>>> Another question: In the web page <BR>>>_group.genebee.msu.su/3d/oplsa_ff.html_ I've found "Add records for <BR>>>RNA 3' and 5' ends (for DNA it has already been added)". What does <BR>>>it means?<BR>>> Thanks in
advance,<BR>>>Vincenzo<BR>>><BR>>>------------------------------------------------------------------------<BR>>>Condivi foto, pensieri ed altro ancora creando il tuo Blog su MSN <BR>>>Spaces. E' gratis! <http://g.msn.com/8HMBITIT/2746??PS=47575><BR>>><BR>>><BR>>>------------------------------------------------------------------------<BR>>><BR>>>_______________________________________________<BR>>>gmx-users mailing list<BR>>>gmx-users@gromacs.org<BR>>>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>>>Please don't post (un)subscribe requests to the list. Use the www <BR>>>interface or send it to gmx-users-request@gromacs.org.<BR>>_______________________________________________<BR>>gmx-users mailing
list<BR>>gmx-users@gromacs.org<BR>>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>>Please don't post (un)subscribe requests to the list. Use the www <BR>>interface or send it to gmx-users-request@gromacs.org.<BR></FONT></BLOCKQUOTE></div><br clear=all><hr> Hai bisogno di una risposta immediata? <a href="http://g.msn.com/8HMBITIT/2743??PS=47575" target="_top">Prova MSN Messenger.</a> </html>