Re: [AMBER] contact analysis with CPPTRAJ

From: Daniel Roe <>
Date: Fri, 15 Jan 2016 09:12:24 -0700


Unfortunately there is currently no straightforward way to get what
you want, which I think is all contacts per frame, yes? The way that
the command is set up you would currently have to script it and parse
the output, something like (bash):

for ((FRAME=1; FRAME <= $NFRAMES; FRAME++)) ; do
  cat >> <<EOF
reference $FRAME
trajin $FRAME $FRAME
nativecontacts writecontacts frame.$FRAME.dat ...


(Note I have not tested above code, just using as an example).

Having the option to write out every potential contact every frame is
something I can look into adding. Note that you can get an idea for
what non-native contacts are forming via the 'map mapout <file>'
option (it will have a nonnative. prefix).

Hope this helps,


On Fri, Jan 15, 2016 at 4:59 AM, anu chandra <> wrote:
> Hello Amber users,
> I am looking for a suitable CPPTRAJ tool that can be used for finding out
> all the contacts between domain 1 (residue 1-200) and domain 2 (201-450) of
> the protein. I am aware of the tool 'nativecontacts' which basically output
> the contacts with respect to the reference structure. Here, I wish to
> output all the conctatcs within a specified cutoff ( say <= 3.5)
> irrespective of whether it present or absent in the reference structure,
> in a similar format as the 'nativeconctas' does with 'writecontacts' flag.
> Many thanks in advance
> Regards
> Anu
> _______________________________________________
> 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 Fri Jan 15 2016 - 08:30:04 PST
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