Thank you Dan for the help!
On Tue, Jul 15, 2014 at 10:17 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The third column is a measure of native contact (positive number) or
> non-native contact (negative number) averaged over all frames. Since you
> have specified byresidue, the first two columns are residue numbers and
> total contacts for the residue are summed over all atom-atom contacts
> between the two residues (which is why you get numbers greater than and
> less than 1).
>
> Hope this helps,
>
> -Dan
>
>
>
> On Tue, Jul 15, 2014 at 5:36 AM, Rajeswari A. <rajeswari.biotech.gmail.com
> >
> wrote:
>
> > Dear Amber users,
> > I did not understand mapfile generated by nativecontacts command in
> cpptraj
> > of amber14. Can someone explain me?
> >
> > I used the following command to calculate the native contacts between
> mask1
> > and mask2 with respect to reference structure.
> >
> > "nativecontacts mask1 mask2 reference distance 6.0 byresidue out
> > contacts.out writecontacts native_list.out map mapout mapfile6.dat"
> >
> > The mapfile has 3 column in which 1st column and 2nd column represents
> mask
> > residues. What does the third column indicate?
> >
> > A portion of map output file is given below
> > 202.000 147.000 0.0000
> > 203.000 147.000 -0.0001
> > 204.000 147.000 -2.7229
> > 205.000 147.000 -12.7986
> > 206.000 147.000 -46.0464
> > 207.000 147.000 0.1499
> > 208.000 147.000 -3.3104
> >
> >
> > Thanks
> > --
> > Rajeswari A,
> > _______________________________________________
> > 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 201
> 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
>
--
Rajeswari A,
PhD Research Scholar,
Computational Biophysics Lab,
Department of Biotechnology,
Indian Institute of Technology Madras,
Chennai 600 036, Tamil Nadu, India.
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Received on Tue Jul 15 2014 - 22:00:02 PDT
