Re: [AMBER] Cpptraj (post-processing rotation)

From: Kenneth Huang <>
Date: Mon, 21 Dec 2020 13:57:16 -0500


I think somthing like this might be what you're looking for- you might have
to fiddle with the atom selection masks for the image part, though

center :1-327
image .WAT
rms first :1-327



On Mon, Dec 21, 2020 at 5:08 AM Женя Елизарова <>

> Dear Amber developers,
> I was trying to remove the rotation of a protein during cpptraj
> post-processing. I used:
> rms :1-327
> but when I looked at the trajectory it seemed like water molecules
> layered on each other. This didn't appear without rms, so I suppose it is
> related to the visualization. Is it possible to post-process files without
> rotation and normal behavior of water molecules?
> Best regards,
> Evgenia Elizarova
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Received on Mon Dec 21 2020 - 11:00:02 PST
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