Re: [AMBER] Structure Artifact After Autoimage

From: Daniel Roe <>
Date: Tue, 4 Aug 2020 09:25:10 -0400


There are a few things that might be going on here, but we need more
information. Has this trajectory been previously rotated somehow, for
example by RMS-fitting to a reference? If so then the coordinates no
longer align with the unit cell vectors and imaging is no longer

If it's not that, could you possibly send me off list the topology and
1 or 2 frames of the trajectory that I can use to reproduce your
issue? Thanks,


On Fri, Jul 31, 2020 at 5:02 PM Mikhael, Simoun <> wrote:
> Hello,
> I use autoimage to center the trajectories of the water box and protein (pentamer) structure. However, I get an artifact that isn't present before I do the autoimage.
> I've attached an image to show the artifact where some of the atoms are flying around the protein structure. Do you know what could be the reason, and how to fix that artifact?
> I use the following commnds:
> cpptraj
> > parm protein.prmtop
> > trajin 1 500 10
> > autoimage
> > trajout autoimage_protein.mdcrd mdcrd
> > run
> Thanks!
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Received on Tue Aug 04 2020 - 06:30:02 PDT
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