my input file (traj.run) is:
"trajin x.trr
stript !(:Me)
trajout x.crd"
and I run this with: cpptraj -p x.pdb -i traj.run
I am going to keep just one atom (methane). How should I know if my
original trajectory has been imaged by atom?
Thanks
Hadi
On Thu, Sep 19, 2019 at 1:50 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> >
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Received on Thu Sep 19 2019 - 12:00:02 PDT
