AMBER Archive (2008)

Subject: AMBER: Steered MD and Jarzynski in pulling simulations

From: Samuel Genheden (
Date: Wed Nov 05 2008 - 08:48:33 CST

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
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