[gmx-users] gramicidin A

Bert de Groot bgroot at gwdg.de
Fri Jan 31 09:49:21 CET 2003

"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.


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

More information about the gromacs.org_gmx-users mailing list