Re: simulation of membrane-protein systems

From: Richard Wood (
Date: Fri Dec 15 2006 - 05:12:26 CST

Hi all, I'm reposting a question that originates more from my curiosity than anything else. Having worked with lipids in the past, I have just started to play around with the membrane generating function of VMD. I notice that one can create POPC or POPE membranes. I have two questions, one for VMD users and one for NAMD users. Will it be possible to create a membrane using DMPC in VMD at some point? Secondly, once you've created a membrane.pdb and membrane.psf, what force field does one use to do computations? Are there CHARMM parameter and topology files out there that have POPC, POPE and DMPC molecules in them? I ask this because I've not done membrane calculations using CHARMM before. I've since answered this second question myself, as I built a membrane in VMD and was able to minimize it using NAMD. I used the parameter file par_all27_prot_lipid.prm. Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:57 CST