Hello,<br><br>More specifically, I am unsure as to the procedure of inflating and minimizing a bilayer using "InflateGRO". In the tutorial at:<br><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html</a><br>
<br>I followed it successfully up to the inflation step, but I do not know specifically what parameters to run the energy minimisation. Please advise.<br><br>Thank you.<br><br>Nancy<br><br><br><br><br><div class="gmail_quote">
On Wed, Jul 29, 2009 at 7:49 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>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am trying to run energy minimisation on a lipid bilayer (downloaded from: <a href="http://moose.bio.ucalgary.ca/files/dppc128.pdb" target="_blank">http://moose.bio.ucalgary.ca/files/dppc128.pdb</a>). I inflated the bilayer using "InflateGRO" however, when I try to run the minimisation, it seems to display the un-inflated bilayer. Please advise.<br>
<br>
</blockquote>
<br></div>
Without seeing the command lines that you're issuing, we can only assume you are doing something wrong.<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;">
Thank you.<br>
<br>
Nancy<br>
<br>
<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
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