[gmx-users] ATP parametrization

[David van der Spoel]

On Mon, 2002-12-16 at 14:19, Bjoern Windshuegel wrote:
> hi guys,
> 
> i'm trying to parametrize some ligands for my simulations. since i have a
> phosphate group in one ligand i tried to use the parametrization as it is
> done for ATP in ffG43a1.rtp. for the dihedrals there are some puzzling
> parameters:
>  
>  AC5* AO5*  APA   AO3PA   gd_11
>  AC5* AO5*  APA   AO3PA   gd_9
> 
> is there any intelligent reason why both dihedrals were chosen? gd_9 as
> well as gd_11 are suited but both together...???? 
Don't know about the history of this, but adding two simple cosines
gives you a different more complex potential, comparable to e.g.
Ryckaert-Bellemans, or the OPLS cosine series.
> 
> best regards,
> 
> bjoern
> 
> 
> 
> 
> 
> 
> Bjoern Windshuegel
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharmazeutische Chemie
> Gebaeude 26.23	               email: windshue at pharm.uni-duesseldorf.de
> Universitaetsstrasse 1	       phone: (49)211 811-2525
> 40225 Duesseldorf                FAX: (49)211 811-3847
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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