Thanks a lot Justin!<br><br><div class="gmail_quote">On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 5/15/12 5:54 AM, Anirban wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi ALL,<br>
<br>
How accurate are the topologies of non-standard molecules generated by ATB or<br>
SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to<br>
carry out manual checks like that required for PRODRG outputs?<br>
Any suggestion is welcome.<br>
<br>
</blockquote>
<br></div></div>
I would always verify parameters before running real production simulations. I believe ATB and SwissParam are, in general, far more reliable than PRODRG, but I doubt it can be stated universally that any automated method is inherently flawless.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
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Justin A. Lemkul, Ph.D.<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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