Dear Prof van der Spoel and GROMACS users,<br><br>I have read the article "Scrutinizing Molecular Mechanics Force Fields..." where it is demonstrated that AMBER99sb yields protein conformations that are in better agreement with residual dipolar coupling, J-coupling and NOE data, compared with other force fields. However, both proteins used for this benchmark study (ubiquitin and protein G) are rather rigid, so I was wondering if there is a similar analysis for flexible proteins/peptides. I want to simulate a few intrinsically disordered proteins/peptides of length between 40 and 100 aa and would like to know what would be the best choice of force field to use. Any experience or knowledge on this matter would be greatly appreciated!<br>
<br>thanks in advance,<br>Thomas<br><br><br><br><div class="gmail_quote">On 27 May 2011 19:01, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5">On 2011-05-27 17.50, simon sham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
I have recently done two simulations on a protein at high temperature<br>
near its melting temperature. At the beginning I used CHARMM forcefield,<br>
and then OPLSAA to double check the results. There are some differences<br>
in the structures between the forcefield used. I know different<br>
forcefields can give different results. All parameters in the<br>
simulations were the same except the forcefield. Is there anyway I can<br>
tell which forcefield gives more reliable results?<br>
<br>
Thanks for the insights,<br>
<br>
Simon<br>
<br>
</blockquote></div></div>
You might want to check<br>
<br>
Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655 (2010)<br>
<br>
where we compare a number of FFs to NMR data.<br><font color="#888888">
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>
<p style="margin-bottom: 0cm;" align="LEFT">======================================================================</p>
<p style="margin-bottom: 0cm;" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom: 0cm;" align="LEFT">PhD student</p>
<p style="margin-bottom: 0cm;" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom: 0cm;" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>
</p>
<br>