Re: [AMBER] nativecontacts resout command change with AmberTools16 [cpptraj]

From: Daniel Roe <>
Date: Tue, 31 May 2016 08:53:33 -0600


It seems like your message may have been truncated, but I did receive
the PDBs of the average structures from both versions of cpptraj. As
you probably already ascertained, the average structures are
identical. My advice is to use the AT16 version of cpptraj. Based on
what you have shown me so far I can't reproduce the behavior (in any
version), and the output you get from the AT16 version seems far more

That said, you may want to think twice before using an average
structure as a reference for determining native contacts. The average
structure is not a real structure; it's utility lies in things like
using it as a reference for fitting to reduce overall rotations etc.
Typically a reference for 'nativecontacts' would be something like a
cluster representative or an experimentally determined structure,
although maybe you have some reason for using the average structure
that I'm just not thinking about.


On Mon, May 30, 2016 at 8:41 AM, Eiros Zamora, Juan
<> wrote:
> Dear Dan,
> I’m a

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)
AMBER mailing list
Received on Tue May 31 2016 - 08:00:03 PDT
Custom Search