Re: [AMBER] trajectory coordinate out of box

From: David A Case <>
Date: Thu, 19 Sep 2019 15:48:42 -0400

On Thu, Sep 19, 2019, Hadi Rahmaninejad wrote:
>I am trying to extract coordinate data of a projectile (a methane molecule)
>using this script of cpptraj:
>-p x.pdb
>trajin x.trr
>stript !(:Me)
>trajout x.crd

Take the time to read carefully what cpptraj reports to stdout. It
should tell you how many atoms are left after the strip command, whether
it understood everything you ask of it (for example, you have a typo
in the strip command above--it's not clear what input cpptraj actually
processed.) Your output somehow looks like cpptraj thinks you have
either zero or one atom in the stripped trajectory.

Try some simple experiments, like changing your trajin command to
'trajin x.trr 1 1 1' which will give you exactly one frame; then
'trajin x.trr 1 2 1' will get you two frames, etc. You could experiment
with adding the "nobox" option to the trajout command. See what happens
if you leave out the strip command. ...etc...

...good luck...dac

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Received on Thu Sep 19 2019 - 13:00:01 PDT
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