AMBER Archive (2009)

Subject: Re: [AMBER] SMD in Amber10

From: Adrian Roitberg (
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:
> Hello!
> 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
                              Associate Professor
                             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

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