[gmx-developers] (no subject)

[David]

On Fri, 2002-11-22 at 18:01, Vibin R wrote:
> Hi
> 	While doing simulated annealing a considerable percentage of the
> structures recovered after cooling is found to be having cis amides, with
> omega angle close to zero value. Can I some artificial means increase the
> value of the force constant, so that the planarity of the amide bond is
> maintained even at higher temperatures. If yes, I guess i may have to make
> changes in ffG43a1bon.itp file. But where exactly should i change and to
> what extent is permissible. 
Do you mean they go from trans to cis? At what temperature?

You can indeed change the force field parameters in the ff*bon.itp
files.
> 
> Expecting your kind attention
>                                         
>  affly
>  Vibin                                                                      
> ******************************************
>  Vibin Ramakrishnan         	
>  De novo design lab
>  School of Biosciences and Bioengineering
>  IIT Bombay                          	
>  Powai,Mumbai-400076		
> ******************************************
> 					
> 
> 
> 
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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://zorn.bmc.uu.se/~spoel
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