Re: building a MARTINI bilayer

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 21 2010 - 13:16:00 CDT

Hi Ed,
Is your question on how to build the all atom or CG configuration? The
all atom configuration can be generated with the vmd membrane builder.
To get the cg conformation, the cleanest way is to make .cgc files like
those for the Shih et al. RBCG model (since MARTINI partitions residues
in a very similar way) and then use the cg plugin. See the section at
the bottom of http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/ for a
brief description of the cgc file format, which is used to specify the
all atom->cg mapping for RBCG models. You should be able to find more
detailed examples in the cgc databases that are in the cgtools directory
of the vmd distribution.

Best,
Peter

Edward Lyman wrote:
> Hi all,
>
> I see that there is available a charmm-formatted param file for the MARTINI
> lipid models. It is also very easy to use the cg plugin to build a residue
> based model of a protein. But what is the fastest way to build a starting
> config for a MARTINI bilayer? Is there a script available for this purpose
> like the one described in the SBCG tutorial? Or do I need to write one?
>
> Thanks,
> Ed
>
>

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