Re: [AMBER] Need help for retrained MD

From: Jason Swails <>
Date: Tue, 07 Oct 2014 07:55:58 -0400

On Tue, 2014-10-07 at 16:07 +0530, Sudhanshu Shanker wrote:
> Dear AMBER users,
> I am trying to put a distance restrain on Mg+ ions from a xyz coordinate
> (which is a middle point of two atoms like :3.N1 and :11.N3 ). I do not
> have any idea to use such type of restrain. Kindly suggest me a way to do
> this.

You can specify groups of atoms when you define a distance restraint.
When you specify a group of atoms, it uses the center of mass, I believe
(it might use the center of geometry, I'm not sure... but when both
atoms have the same mass those two are the same).

There are more details in the NMR chapter of the Amber manual, and you
can find an example in $AMBERHOME/test/nmropt/pme/distance_COM. The
second restraint in that example defines a distance between atom 1237
and the center of mass of atoms 1171, 1169, and 1175.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 07 2014 - 05:00:03 PDT
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