[gmx-users] ligand docking

Berk Hess gmx3 at hotmail.com
Wed Mar 6 14:59:49 CET 2002

The pull code can do what you want.
It can restrain the distance between the centers of mass of
two groups of atoms. If you choose one atom for each group
you get the distance between a pair of atoms.

If your ligand topology can be generated by pdb2gmx you can
also use distance restraints or a harmonic potential (bonds type 6,
see the manual). You can use pdb2gmx -merge to merge the protein
and ligand into one molecule definition. Then you can define
interactions between the two molecules.


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