Re: simulation of membrane-protein systems

From: JC Gumbart (
Date: Wed Dec 13 2006 - 14:42:24 CST

As for new membrane types in the VMD plugin, it is certainly
possible, but when it will be implemented is undetermined. However,
for some bilayer compositions, you can find already-made pdbs on the
internet (for example, I think Scott Feller has a few).

Most membranes can be handled by CHARMM. The default parameter file
can be used; as for topology, I think POPC, POPE, and maybe DMPC are
included verbatim in the CHARMM topology. You can also build other
lipids from fragments present in the topology files (all on Alexander
Mackerell's website). Our Topology File Tutorial provides pretty
good instructions if you wanted to attempt building your own lipid

On Dec 13, 2006, at 2:21 PM, Richard Wood wrote:

> Hi all,
> This question poses a question 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 know some of you may yell at me for not "doing my homework"
> before I ask this...
> Richard
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> Have a burning question? Go to Yahoo! Answers and get answers from
> real people who know.

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