Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?

From: Daniel Roe <>
Date: Thu, 31 Oct 2013 09:59:24 -0600


On Thu, Oct 31, 2013 at 9:45 AM, Jose Borreguero <> wrote:
> I am interested in Eab only. Thus, it would seem I have to get a parm +
> trajectory for only atoms from group A in order to get Ea (and similarly
> for group B), then do Eab=E-Ea-Eb?

This is correct. FYI, in cpptraj you can also use the 'outprefix'
keyword to print a stripped topology file that is compatible with your
stripped coordinates. For example:

parm AB.parm7
strip :A outprefix B

will generate B.AB.parm7, which will be compatible with the output
trajectory Make sure you are using an up to date version of


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 31 2013 - 09:00:05 PDT
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