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,
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>
--
-------------------------
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)
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Received on Tue Jul 15 2014 - 10:00:02 PDT
