AMBER Archive (2008)

Subject: Re: AMBER: Steered MD and Jarzynski in pulling simulations

From: M. L. Dodson (
Date: Wed Nov 05 2008 - 09:04:23 CST

Samuel Genheden wrote:
> Hello, Amber users
> I would like to do some pulling simulation where I drag a small
> molecule (e.g. a drug) away from a macromolecule (e.g. a protein) in
> order to calculate the binding energy. I have read the literature so
> I'm well aware how to do it in theory. However I have some questions
> regarding how to do it in Amber 10.
> I have to apply two restraints, one to the drug and one to the
> protein. The restraint of the drug should be time-dependent and it is
> pretty clear how to set this up by reading the Amber manual. However I
> also need to have a fixed restraint on the protein center-of-mass in
> order to prevent it from "going with" the ligand. How do I setup this
> restraint in Amber 10? Is it done implicitly? I mean, it is rather
> useless to be able do drag one part when the other part is not fixed.
> Regards, Samuel Genheden
> Lunds university, Sweden

You can use regular "NMR-style" restraints together with SMD. Just be
sure that the steered restraint is the first in the list.
Alternatively, you can use the "NCSU" (Adaptively Biased MD)
capabilities in Amber10. This kind of approach can also coexist with
"NMR-style" restraints. See Tutorial A10: . You
would probably use a simple distance (type = DISTANCE) reaction
coordinate as described in the Amber10 documentation (p123) rather
than the LCOD coordinate described in the tutorial. (LCOD is actually
an Amber11 capability, although the patch described in the tutorial
brings the capability to Amber10.)

Bud Dodson

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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