[gmx-users] gramicidin A

[Bert de Groot]

"David L. Bostick" wrote:
> 
> I am interested in simulating the HD form of gramicidin.  I started looking
> into building the topology, but decided to look around first.  It seems
> that it has already been simulated using GROMACS:
> 
> Biophys J Vol 82, June 2002 pp. 2934-2924
> 
> by de Groot, Tieleman, Pohl, and Grubmuller.  The abberant parts of the
> topology are at the termini.  There is a formyl group on one end and an
> ethanolamine group on the other.
> 
> Is there a set of building block files out there with these residues
> included ... or even a topology of a single monomer of GA?  I can just dig
> in myself, but I thought I'd ask around first ... it doesn't hurt to ask.
> 

yes we have a gA topology that you may use. I'll send you the files directly,
to prevent overloading the list.

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________