From: Nicolas Sapay (
Date: Fri Jun 18 2010 - 08:25:09 CDT


 From a pure molecular mechanics point of view, a hydrophobic
interaction is hard to define. A first approach would be to simply check
the contacts between your ligand and the amino acids considered as
hydrophobic (Leu, Ile, Phe, ...). You can do that with the "measure
contacts" command.


P.-S. Reposting a message is considered as extremely annoying on most
mailing list, forum, etc.

ban arn a écrit :
> Dear All
> I am interested in calculating the residues that are involved in
> hydrobhoic interaction with ligand over the trajectories. Is it is
> possible in VMD.
> Kindly advice.
> Many Thanks
> Balaji