Hi Daniel,
Many thanks for your reply.
Anu
On Fri, Jan 15, 2016 at 4:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
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Received on Fri Jan 15 2016 - 09:30:06 PST
