Thanks Angel and Justin.<div>Will try out the options!</div><div><br></div><div>Regards,</div><div><br></div><div>-Anirban<br><br><div class="gmail_quote">On Tue, May 1, 2012 at 5:46 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="im"><br>
<br>
On 5/1/12 8:05 AM, Ángel Piñeiro wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I guess there are better solutions but an alternative is to map your bilayer to<br>
MARTINI (<a href="http://md.chem.rug.nl/cgmartini/" target="_blank">http://md.chem.rug.nl/<u></u>cgmartini/</a>) and then to use SUGAR-PIE<br>
(<a href="http://smmb.usc.es/sugarpie/sugarpie.php" target="_blank">http://smmb.usc.es/sugarpie/<u></u>sugarpie.php</a>) to go to from MARTINI to all-atom<br>
CHARMM36.<br>
<br>
</blockquote>
<br></div>
Even simpler would be to fix the offending atom names and build a suitable .hdb entry (if one does not already exist) and produce the topology with pdb2gmx. I would think it would then be far easier to preserve the original configurations of the lipids, rather than changing the resolution back and forth.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hope it helps,<br>
<br>
Ángel.<br>
<br>
<br>
On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi ALL,<br>
<br>
<br>
I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS<br>
ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using<br>
CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions<br>
(N, P, C, O) between this two FFs as a result of which pdb2gmx gives error.<br>
Can these atom names (hydrogens can be ignored) of my equilibrated POPC<br>
bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in<br>
advance.<br>
<br>
<br>
<br>
<br>
Regards,<br>
<br>
<br>
Anirban<br>
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-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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==============================<u></u>==========<div class="HOEnZb"><div class="h5"><br>
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