AMBER Archive (2009)
Subject: Re: [AMBER] SMD in Amber10
From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Mar 12 2009 - 13:46:14 CDT
Short answer, NO there is no such thing in the SMD code.
However, it does mot matter.
What you need to do is PUSH the ligand out of the pocket.
This is substantially more physical that pulling from outside.
Dmitri Nilov wrote:
> Is there facility to pull ligand from active site in Amber10?
> I mean steered molecular dynamics when external harmonic force is applied,
> in other words a "spring" connected
> to ligand is retracted in certain direction with constant velocity.
> I can`t get clear answer from Manual and mailing list. Could you help me?
> Dmitri Nilov,
> Lomonosov Moscow State University
> AMBER mailing list
Dr. Adrian E. Roitberg
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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