VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Fri Jul 10 2009 - 10:47:00 CDT

Hi,

Indeed, currently the plugin has parameters for only a few lipids.
However, it is rather easy to make a parameter file for the lipid
molecule you need. The assignment of CG beads is described in the
original Marrink's paper,

Marrink, S. J.; de Vries, A. H.; Mark, A. E. J. Phys. Chem. B
2004,108, 750-760

You can also check out our first paper on the topic, which has a short
description of the bead assignment to lipids according to Marrink's
model:

Coarse grained protein-lipid model with application to lipoprotein
particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus
Schulten. Journal of Physical Chemistry B, 110:3674-3684, 2006.

Just do this by analogy to the existing CG models of the available
lipids.

> Also, there are no cgc files for lipid and ions.

Preparing your own cgc file is also very easy. It's described here
(see at the bottom):
http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/

Best,

Anton.

On 10 Jul 2009, at 09:20, Xiang Yu wrote:

> Dear all:
>
> In VMD-plugins cgtools 1.0, I could not find parameters for many
> lipids like DPPC, DPPE, DPPS et,al. Also, there are no cgc files for
> lipid and ions. Is anyone could provide me these files or teach me
> how to update them?
>
> Thank you,
>
> Xiang Yu