Hello,

I am a graduate student using D.S.2.1 for docking small molecules onto a binding site.  I am having some trouble using LibDock.  I want to restrict certain poses of the ligand in the binding site, but I am not sure how to do so.  For example, I want to restrict a certain portion of the ligand to bind to a residue on the protein (i.e. phosphonate group with a serine residue).  I just want it to be within a certain vicinity of the residue.  Everytime I run the docking simulation, it always outputs docked poses that are not close to the true fit of the ligand.  Any help would be appreciated.

-AK

Note: no one else at either University knows how to run the software, so my help is limited.