From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Wed Mar 18 2009 - 11:42:46 CDT
(Hm, I replied to this email but instead to the mailing list it went to
the OPs email address. Would it be possible for the list administrators
to set the Reply-to accordingly?)
On Wed, 2009-03-18 at 16:51 +0200, doty alexiou wrote:
> I am trying to run an MD simulation of a CG protein model folding
> using NAMD.Where could i find a sample of a configuration script using
> periodic boundary conditions?Is it possible with this method to obtain
> the tertiary structure of the protein?I am a little confused because
> although i read that cg-method is used in protein folding studies i
> also found some documents where it is said that its not posiible to
> obtain the tertiary structure with this model.So, what should i be
> careful or do more?Thank u.
There are certain CG models that have been designed with protein folding
in mind I believe. Others like the ones derived from MARTINI have a
hard time of even keeping the proper tertiary structure and I would be
very surprised to see that they would be useful in protein folding. For
the MARTINI force field for proteins itself the knowledge of the
secondary structure is required as a prerequisite as it is needed to
determine the parameters. The secondary structure is then (more or less)
kept during the simulation.
Hannes.
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