Hi,
Its not clear to me what you’re doing exactly. Are the trajin, strip, and
trajout commands in an input file or are you running cpptraj interactively?
How many atoms are you expecting to keep (is it 4 - a single methane)? Is
your original trajectory imaged by atom perhaps?
-Dan
On Thu, Sep 19, 2019 at 12:47 PM Hadi Rahmaninejad <ha.rahmaani.gmail.com>
wrote:
> 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 - 11:00:02 PDT
