Hello Amber Users,
I am trying to extract coordinate data of a projectile (a methane molecule)
using this script of cpptraj:
cpptraj
-p x.pdb
trajin x.trr
stript !(:Me)
trajout x.crd
and I am getting data in three column, but it seems they are not in order
of (x y z). Moreover, sometimes in some lines I see that it give the
coordinate out of the boundary of my box, as I set my simulation to be
under "periodic boundary conditions". Here is a few lines of data I am
getting:
Cpptraj Generated trajectory
55.977 57.708 56.110
111.547 111.547 111.547
55.804 57.936 56.225
111.580 111.580 111.580
64.527 60.071 61.458
144.687 142.126 141.330
48.731 45.430 61.840
182.066 181.318 182.398
56.097 64.419 91.501
177.690 177.337 134.112
58.329 69.342 90.181
139.494 163.174 163.994
I tried to use autoimage after my trajin line, but it is not working. I
highly appreciate if any one can give me some hints,
Thank you,
Hadi
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Received on Thu Sep 19 2019 - 10:00:02 PDT
