Hi Oliver,<br><br>Apologies for the late reply. The comparison you have showed us has been done for a DNA fragment. Do you believe that negligible errors can also be obtained for proteins using the amber99sb force field? <br>
<br>thanks,<br>Thomas<br><br><br><br><div class="gmail_quote">On 22 November 2011 11:58, Oliver Grant <span dir="ltr"><<a href="mailto:olivercgrant@gmail.com">olivercgrant@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi there,<div><br></div><div>Acpype does the conversion for you and the results from their own testing are here:</div><div><a href="http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx" target="_blank">http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx</a></div>
<div><br></div><div>For reproducing experimental data I would look in the original force-field publications.</div><div><br></div><div><font color="#888888">Oliver</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">
On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts <span dir="ltr"><<a href="mailto:mrshirts@gmail.com" target="_blank">mrshirts@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>> Is anyone aware of any benchmark analysis about the implementation of the<br>
> amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in<br>
> GROMACS and AMBER. I am interested to know in what extend the energies<br>
> correlate and if the results agree with experimental data.<br>
<br>
</div>Whether the results compare agree with experimental data is irrelevant<br>
to the correctness of the implementation -- that has to do with the<br>
validity of AMBER99sb to begin with. The only question is, do GROMACS<br>
and AMBER give the same energies for the same configurations?<br>
<br>
I actually do not know the answer, and would be interested to hear if<br>
it's been tested. <a href="http://ffamber.cnsm.csulb.edu/" target="_blank">http://ffamber.cnsm.csulb.edu/</a> does not appear to<br>
have the very comprehensive tests that appear for earlier models at<br>
the current time. I SUSPECT there should not be a problem, since<br>
AMBER99sb just changed a couple of torsions, so errors are unlikely<br>
(though in theory possible).<br>
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<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
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