Hi,
The new 'nativecontacts' command in cpptraj will automatically image
distances unless the 'noimage' keyword is used, so any contacts
(native or non-native) that are across periodic boundaries should be
picked up. Let me know if you encounter any issues with it. Good luck,
-Dan
On Wed, May 21, 2014 at 1:19 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> wrote:
> Hello Amber community,
>
> I was wondering if cpptraj has a functionality for calculating
> intermolecular contacts across periodic boundaries. I am doing simple
> single-protein-in-a-water-box simulation and am curious if any of the
> protein residues are influenced by residues *from the periodic images *(to
> make sure the water box is large enough)*. *Such analysis is trivial enough
> to do outside of AMBER for a rectangular box, but I am using a truncated
> octahedron, and so was wondering if this functionality already existed?
>
> Thank you,
> Eugene Yedvabny
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed May 21 2014 - 14:30:02 PDT
