<br><br><div class="gmail_quote">On Tue, Apr 6, 2010 at 5:05 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>
Arun kumar V wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file.<br>
<br>
</blockquote>
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If by "be careful" you mean "don't use this topology," I'll agree :) The Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1, given by PRODRG) fall far short of reproducing lipid properties. That, and the charges assigned by PRODRG for lipids will not resemble any known parameter set, requiring a complete re-write of this topology. You could use PRODRG to build the molecule, but there are a number of other programs that can do that as well (see the Gromacs site for a list).<br>
<br>
To the original post: What lipid are you looking to simulate? Many pre-equilibrated lipid bilayers are available in the public domain, along with suitable paramters, saving you a lot of work in building these systems. They can be tricky.<br>
<br>
-Justin<div class="im"><br>
<br></div></blockquote><div>@Justin<br> I agree with you. Currently I am not actively involving with gromacs simulations but planning to involve. I have not been to GROMACS website from long time. In fact the version I have used last time is gromacs 3.3(almost 2 years back). There is lot of progress ofcourse. <br>
</div><div> </div><div>Thanks,<br>Arun<br><br></div><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">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Arun<br>
<br>
Saumya 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 all,<br>
<br>
Well, I have been trying to make lipid bilayers using genconf of<br>
gromacs from a single lipid molecule.<br>
Can anyone tell me how to proceed with the simulation of lipid<br>
bilayers starting with a single lipid molecule?<br>
How can I obtain the .pdb file for a lipid?<br>
Is there any manual that describes the procedure using Gromacs?<br>
<br>
Hoping for some inputs.<br>
<br>
Regards<br>
Saumya<br>
<br>
</blockquote>
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</blockquote>
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-- <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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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Arun<br>