<div dir="ltr">I was working with protein complex, and after tests some FF, I could obtain best results with oplss/aa <br><br><div class="gmail_quote">On Wed, Sep 10, 2008 at 12:07 PM, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr"><br>Short answer, try Amber99SB with Gaff.<br><div class="gmail_quote"><div><br>
Alan <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Message: 1<br>
Date: Fri, 5 Sep 2008 15:06:21 +0200<br>
From: " Paula Gonz?lez-Rubio " <<a href="mailto:paula.grg@gmail.com" target="_blank">paula.grg@gmail.com</a>><br>
Subject: [gmx-users] which force field for a protein-protein complex?<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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Hello there,<br>
<br>
I would like to do a MD of a protein-protein complex (both with their<br>
ligands) so I'm looking for some advise regarding the best force field for<br>
simulate my system. For more details, it consists on a ADP-ribosylase (which<br>
ligand is the NAD) and a small G protein (GDP binded), we want to see what<br>
is the role of a loop in the formation of the complex and on the<br>
ADP-ribosilation of the small G protein.<br>
<br>
Does any one have a good idea of an appropiate force field for this kind of<br>
systems ? Do you think gromos 43A1 or ffgmx could be an option?<br>
<br>
Thanks a lot in advance!<br>
Paula<br>
<br>
<br>
-- !!!!! NEW email !!!!!!<br>
<br>
<a href="mailto:paula.grg@univ-paris-diderot.fr" target="_blank">paula.grg@univ-paris-diderot.fr</a><br>
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--</blockquote></div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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