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

[Santi Esteban Martin]

 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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