namd: DSPC and DAPC for a phospholipid bilayer

From: SMAHANE CHALABI (smahane_chalabi_at_hotmail.com)
Date: Fri Apr 20 2007 - 04:55:21 CDT

Hi,

I am currently doing a training period within my Master of science and
Computational Biology at Evry, in France. This one consists in Molecular
modeling and drug design, and I will have to use Visual Molecular Dynamics
to simulate a membrane biologic. So, Iíll have to use unusual phospholipids
such as distearoylphosphatidylcholine (DSPC) and
diarachidoylphosphatidylcholine (DAPC).

However, VMD version 1.8.6 is able to generate a phospholipid bilayer
composed by POPE or POPC as we can see in the text consol window such as:

Usage: membrane -l <lipid> -x <xsize> -y <ysize> {-o <prefix>}
<lipid> is lipid name (POPC or POPE; others as added)
<xsize> and <ysize> are membrane sizes in X and Y (Angstroms)
<prefix> is optional output file prefix (default "membrane").

However, I donít know how to construct the template box structures for DAPC
and DSPC. So, I would like to ask you if anybody has already been confronted
to a such problem.
I have seen that there is a combined CHARMM All-Hydrogen topology file for
proteins and lipids, which contains POPC and POPE topologies.
Would I have to create a topology file for DSPC and DAPC? and/or is there an
other way to construct this box structures?

Thanks very much for your answers!!

Yours sincerely,
Smahane CHALABI

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