It is on now,you can use it.<br>as Justin said you should validate it.<br>best<br><br><div class="gmail_quote">On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
C.Y. Chang wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I need to obtain the GROMOS96 topology files (and including the corresponding PDB files) for some small molecules.<br>
I could obtain them from PRODRG beta server before, but the server seems to shut down now.<br>
</blockquote>
<br></div>
According to the site, it will be up within 24 hours. PRODRG is a fine tool, but should not be viewed as sufficient to produce reliable topologies in the absence of further validation and almost certain refinement.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
How could I get them? or from other server or program?<br>
</blockquote>
<br></div>
Regardless of how you produce your topologies, you should understand the intrinsics of the force field so you can do proper validation.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br>
<br>
Pay special attention to the second link and the referenced material.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Chia-yun Chang<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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.vt.edu/Pages/Personal/justin</a><br>
<br>
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