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

[Kay Gottschalk]

Depends on the size of the molecule and the number of NOE data you 
have. A specialized program for this kind of calculation is CNS (a 
newer version of XPlor). There you can also add things like chemical 
shift restraints (perhaps not so meaningful for non-protein compounds), 
dihedral angle restraints  - basically everything you can measure with 
NMR. CNS is significantly slower than Gromacs, but if your system is 
small, it is o.k. And it has scripts for structure calculation by NMR 
(like simulated annealing and stuff). Topologies are always a problem.
K.

On Jan 12, 2004, at 3:07 PM, 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.
>
>
>  Thanks to everyone!
>
>
>
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