[gmx-users] GDP Topology
cseifert at bph.ruhr-uni-bochum.de
Tue Jul 22 13:49:36 CEST 2008
On Mon, 2008-07-21 at 11:49 -0600, Travis Craddock wrote:
> Hello all,
> I am trying to make an addition to mu ffG43a1.rtp file for the molecule GDP.
> I have read the entry:
> which gives the topology for GTP. I would like to know how the parameters for
> the GTP topology were found so that I may extend them to GDP.
You should delete the beta-phosphate and fix the bonds, angles, etc.
For MM calculations this approximation is ok:
GDP beta phosphate = GTP gamma phosphate
> Travis Craddock
> Department of Physics
> University of Alberta
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M. Sc. Christian Seifert
Department of Biophysics
University of Bochum
Tel: +49 (0)234 32 28363
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E-Mail: cseifert at bph.rub.de
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