Re: [gmx-users] Which POPC Bilayer to start?

[Jim Fonseca]

I've had success with Tieleman's lipids.  I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems.  However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM & PR). Jim On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote: Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer >>>> 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre-equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: [EMAIL PROTECTED] Tel: 662-915-1286 (office); Web: www.olemiss.edu _______________________________________________ gmx-users mailing list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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