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

Santi Esteban Martin sanesmar at alumni.uv.es
Mon Jan 12 14:09:01 CET 2004

 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!  

Universidad de Valencia, SPAIN.
Departamento de Bioquímica y Biología Molecular
C/ Dr. Moliner, 50.
46100 Burjassot (Valencia)
PHONE: +34 963543797   FAX: +34 963544635
URL: http://mural.uv.es/sanesmar

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