From: Niklaus Johner (nij2003_at_med.cornell.edu)
Date: Fri Mar 29 2013 - 08:39:05 CDT
This isn't strange, it just means your ligand is not stable in the binding-site. The most likely problems in my opinion are either your force-field, your docking pose or your equilibration procedure.
What force-field are you using? From what I know using gaussian for parameterization gives partial charges that aren't necessarily compatible with the CHARMM force-field. Maybe run a simulation of just the solvated ligand, to make sure your dihedral terms are ok and that it samples the conformations you expect.
If you are confident in your binding pose, parameters and equilibration procedure, then maybe the implicit solvent representation isn't good enough for that particular case, so try to run an explicit solvent simulation.
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On Mar 29, 2013, at 9:00 AM, Fugui wrote:
I used implicit solvent to do a MD of a protein-ligand complex, however, i got a very strange result. The ligand came out of the binding pocket. I used gaussian03 to produce the force filed of the ligand, i have no idear about the reason , could anyone give me some advices?
By the way, i got strange results using 999 and 16 for cutoff.
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