Hi,
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 >> cpptraj.in <<EOF
reference mytraj.nc $FRAME
trajin mytraj.nc $FRAME $FRAME
nativecontacts writecontacts frame.$FRAME.dat ...
EOF
done
(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,
-Dan
On Fri, Jan 15, 2016 at 4:59 AM, anu chandra <anu80125.gmail.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 15 2016 - 08:30:04 PST
