Re: [AMBER] Calculation of Urea_Urea Interaction energy

From: Daniel Roe <>
Date: Mon, 8 Sep 2014 07:44:56 -0600

On Mon, Sep 8, 2014 at 5:49 AM, Jason Swails <> wrote:
> >From everything that I can tell by looking at the code, the 1-4
> electrostatic and van der Waals interactions are completely excluded
> (that is, they're not included in any energy contribution that is
> printed above). I know the 1-4 pairs are in the exclusion list, and
> there seems to be no code handling 1-4 interactions specifically (so I
> conclude that they must be omitted).

This is correct, 'pairwise' does *not* include 1-4 pairs. It only
calculates the VDW/EELEC terms of the Amber force field, taking into
account the the excluded atoms lists. The original reason I wrote the
'pairwise' command was to compare how the strength of specific
non-bonded interactions in some reference change in some target
structure (i.e. do certain pairs get stronger/weaker, is it mainly a
van der Waals or electrostatic change, etc).

While there are plans to include some basic energy analysis in cpptraj
in the future, for now if you need detailed energy analysis you are
better off using sander (freely available with AmberTools 14) and
trajectory post-processing (imin=5).


> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 08 2014 - 07:00:04 PDT
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