Re: [AMBER] Contact analysis using cpptraj

From: Daniel Roe <>
Date: Wed, 13 Jan 2016 10:10:15 -0700


I believe you can get the output you want using the cpptraj
'nativecontacts' command, something like:

nativecontacts name NC2 :10-14.CA :17-21.CA out \
                      mindist maxdist writecontacts nc2.contacts.dat \
                      resout nc2.res.dat

In this example I'm using two masks to restrict the search to contacts
between two regions, but you can also use just 1 mask. See the manual
for further details. Hope this helps,


On Wed, Jan 13, 2016 at 8:25 AM, Kucharski Jr., Amir N
<> wrote:
> Hi,
> I am trying to use the contacts analysis tool in cpptraj in order to see what residues are contacting. That is, I would like to get data that reports something along these lines:
> "res1 res2 X%" , where X% is the percentage of time from the CHARMM dcd that the C-alpha atoms of res1 and res2 are within the cutoff distance. I tried using the byresidue tag and that did not work. Any help is much appreciated.
> Thanks,
> Amir
> _______________________________________________
> 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 Wed Jan 13 2016 - 09:30:05 PST
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