[gmx-users] GDP Topology

[Christian Seifert]

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:
> 
> http://www.gromacs.org/pipermail/gmx-users/2007-December/031139.html
> 
> 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

Greetings,
Christian.

> 
> Thanks,
> Travis
> 
> 
> Travis Craddock
> Department of Physics         
> University of Alberta
> 
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-- 

M. Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
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E-Mail: cseifert at bph.rub.de
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