Re: ligand flies away from binding pocket

From: Chris Harrison (
Date: Fri Feb 13 2009 - 18:07:44 CST


Mert is correct, and this approach can and has been used successfully by
many. HOWEVER, before you blindly do this, I would strongly suggest you
troubleshoot your problem further and answer WHY your ligand is trying to
unbind. Assuming binding occurs in the experimental system with sufficient
affinity to persist beyond the timescale of your simulation, it is more
likely that something is either missing or wrong with your parameters,
conformation, setup, etc. You should elucidate what is causing the
unbinding and determine if it is consistent or orthogonal with reality
before deciding to take the non-physical sledgehammer route. ;)


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Thu, Feb 12, 2009 at 11:39 AM, Osman Yogurtcu <>wrote:
> Hi,
> I have a 300 K water NPT simulation of a ligand (one aminoacid) bound to a
> receptor. After I do minimization and equilibration (for 1 ns), I do an MD
> run. I observe that my ligand leaves the binding pocket after 2 ns.
> My question: is there a trick that I can make sure that my ligand sits in
> the binding pocket all the time or should I define bonds artificially and
> fix the ligand?
> thank you,
> Osman

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