Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin

From: Nathan H. Cho (nate1_at_mbi.ucla.edu)
Date: Wed Dec 20 2006 - 20:59:20 CST

Hello. I'm an experimentalist trying to perform a molecular dynamics
simulation to get an idea of how DMPC, CHAPSO, and SDS molecules are
oriented around the native state of a membrane protein, bacteriorhodopsin.
Eventually I would like to run an MD simulation of a number of those lipid
and detergent molecules (around 40 DMPC, 16 CHAPSO, and 84 SDS molecules)
and explicit waters around a single constrained protein within a box.

Here's the first problem I ran into. There is no CHARMM topology/parameter
files available for CHAPSO molecule. I tried to generate them using XPLO2D
from a PDB file that I created, but found out that XPLO2D was very buggy
and didn't yeild usable topoloty/parameter files. My question is, is there
any other way (preferably an easy way) to create topology/parameter files?

I will appreciate any help or tip and acknowledge them. Also, I attach the
PDB file of CHAPSO molecule just in case any of you is interested in the
structure. . . and perhaps interested in creating topology/parameter
files for fun. =)

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