[gmx-users] Nucl. Acids Force-Field Importation???

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 1 18:40:57 CET 2002

On Fri, 1 Mar 2002, Patrick Ladam wrote:

>GROMACS seems above all proteins oriented and its force-field not up-to-date for
>Nuc. Acids
>(what I read at least in a mail of the mail-list).
>So I plan to import the CNS dna-rna-all-atom param and top files in GROMACS,
>possibility would be to import AMBER FF.

That sounds great. 

>What is your opinion about this and what would be the best way to do it?
>Simply translate the CNS files into a  ff*.rtp file?

It would be nicest is you could indeed make a program (preferably C 
or Perl) to transform the force field files into gromacs format. In the 
not so distant future I will start to transform all these kind of data 
files into XML, but then I will have to convert the old files 
automatically as well. It would be nice if we had some kind of CNS input 
reader that we could hook into this conversion tool, such that we can 
convert future CNS and or AMber force fields into gromacs without 
intermediate steps.

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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