Hi justin,<br>Thank you very much for your quick reply. I also want to know is there any other option than PRODRG to generate topology files for the non-standard residues ?<br>As PRODRG server usually go down these days.<br>
<br>With thanks,<br>Vivek<br><br><div class="gmail_quote">2009/3/2 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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="Ih2E3d"><br>
<br>
vivek sharma 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 There,<br>
I am trying to do energy minimization of some protein molecule, and I have following queries for the same.<br>
1. Can I define some RMSD tolerance, such that RMSD value of the molecule during the energy minimization will not vary more than some predefined value.<br>
</blockquote>
<br></div>
No, nor would it do much good. Do you expect the RMSD to change much during EM? I usually see an RMSD no greater than 0.2 Ang.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2. Which integrator is better to use SD or CG ?<br>
</blockquote>
<br></div>
That depends on your definition of "better." Try both and see which results you think are more reliable, otherwise consult some textbook material or literature references on the algorithms.<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
3. what algorithm should be used for long-range electrostatic interaction PME or cut-off.<br>
<br>
</blockquote>
<br></div>
PME is more accurate than cut-off.<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;"><div class="Ih2E3d">
Please suggest for the above queries.<br>
<br>
With thanks,<br>
Vivek<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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>
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