[AMBER] Imaging issue

From: Michael Criddle <mcriddle90.yahoo.co.uk>
Date: Mon, 7 Jul 2014 10:24:49 +0100

Hi all,

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'. Correct visualisation is briefly restored when the ligand 'jumps' back to the original side of the simulation box, but another 'jump' means this is short-lived. I am confused as to what could be the cause of this as the ligands behave perfectly up to this point, and even beyond this point, remain in an orientation conducive to the 'left behind' atom being in the correct position. I am therefore, convinced that this is purely a visualisation issue but I have not heard of cases where molecules are only partly correctly re-imaged.

Is there any other visualisation commands I can try to use in cpptraj? Any help with this issue would be greatly appreciated!
Michael Criddle, PhD Research Student
Jonathan W. Essex Group
School of Chemistry
University of Southampton
Highfield, Southampton, SO17 1BJ
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Received on Mon Jul 07 2014 - 03:00:02 PDT
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