Re: [AMBER] Imaging issue

From: David A Case <>
Date: Mon, 7 Jul 2014 07:47:12 -0400

On Mon, Jul 07, 2014, Michael Criddle wrote:
> I have generated a 500ns trajectory of a protein with two bound ligands
> (PBC, iwrap=1). The trajectory proceeds as normal resulting in one of
> these ligands dissociating from the binding pocket, sampling the protein
> surface and ultimately leaving the simulation box altogether. This
> problem is resolved using the image command in cpptraj, to reimage the
> dissociated ligand back into the simulation box.
> The subsequent visualisation of the simulation appears normal up until
> about halfway when the ligand dissociates from the protein surface
> altogether. Upon the first need to 'jump' to the other side of the
> simulation box, all but one of the atoms of the ligand perform the
> jump, leaving behind a nonsensically long bond bisecting the simulation
> cell to the atom that was 'left behind'.

What arguments did you give for the image command? Is your ligand made up of
more than one residue? Is there anything unique or unusual about the atom
that is not being wrapped?


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Received on Mon Jul 07 2014 - 05:00:03 PDT
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