[gmx-users] Ligand often slips out from the binding site in MD; is it natural?

Shanjie Huang suibingkuai at 123mail.org
Sun Mar 26 10:07:16 CEST 2006

I am doing MD of a ligand-protein complex derivated from docking, but I
found that often the ligand slipped out slowly from the binding pocket.
I then performed some MD simulations of several complex ligand-receptor
complex obtained from PDB database, but no similar phenomena was

Is it natural for a ligand to slip from pocket frequently? Or does it
indicate that my complex model derivated from docking is unreasonable?
What should I do? Thanks to all.

Shanjie Huang
  Shanjie Huang
  suibingkuai at 123mail.org

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