[gmx-users] mixing NOE data and MD for non-protein compoud

[David van der Spoel]

On Mon, 2004-01-12 at 14:07, Santi Esteban Martin wrote:
>  
> 
>  Hi everyone,
>  I am a very great begginir in MD. I have started working with GROMACS
>  and I would like to be advised about my current task:
>  Getting "structure" of a small molecule, more or less: 
>  phe-sugar-sugar-cholesterol by implementing distances restraints
>  from NOE data and running MD with GROMACS.
>  
>  Can I construct gromacs files using PRODRG(taking into account 
>  hydrogens) and using the NOE distances restraints to run MD ?
>  
>  I would appreciete suggestions and any kind of advise.
>  My fears are both about the reality of constructing topology files for 
>  molecules that are not proteins/R,DNA in GROMACS and the possibility 
>  of using only NOE data to "fold" such sort of compound.
> 
Yes. You have two problems/tasks. First is to get a decent topology,
using prodrg. Second is to write a list of NOEs. These you add manually
to the topology (chap. 5), and then it should work.

>  
>  Thanks to everyone!  
>   
> 
> 
> --
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> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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