Re: [AMBER] Cpptraj extracting coordinate data of a projectile

From: Daniel Roe <>
Date: Thu, 19 Sep 2019 06:55:12 -0400


parm <topology file>
trajin <trajectory file>
strip !(<mask selecting methane>)

Notice the “not” (!) in the mask to ‘strip’ effectively changes it to

Hope this helps,


On Thu, Sep 19, 2019 at 12:05 AM Hadi Rahmaninejad <>

> Hello Amber Users,
> I hope you are doing well. I am trying to extract coordinate (x,y,z) data
> as a function of time of a projectile (a Methane molecule) from my
> trajectory data of my gromacs trajectory file (actually it doesn't matter
> as it can act like an amber trajectory file). Is there any function in
> Cpptraj that can do this for me? I used to do this in vmd, but I prefer to
> do in Cpptraj as every thing in cpptraj is quicker (and more reliable). I
> highly appreciate if anybody can help me with this,
> Best,
> Hadi
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Received on Thu Sep 19 2019 - 04:00:01 PDT
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