Re: [AMBER] imaging problem

From: Daniel Roe <>
Date: Mon, 7 Jul 2014 08:16:24 -0600


It sounds like your box is relatively small compared to your system size,
which (as you found) makes imaging very difficult. With autoimage you want
to try and choose a molecule that is closest to all other molecules as your
'anchor'. By default cpptraj tries the first molecule, which is not always
appropriate. Have you tried setting one of your other molecules as the

Without knowing what your system looks like I can only offer general
advice. If you could provide me (off list) with some structures or at least
some pictures that illustrate the problems you are having I may be able to
make better suggestions.


On Sun, Jul 6, 2014 at 3:41 PM, Jonathan Gough <>

> Hi All,
> Does anyone have any experience re-imaging a multi protein/peptide system
> that is in a rectangular box?
> We are attempting to re-image thee production files of a md trajectory and
> are having issues getting the system to stay within the periodic box.
> the major issue, turns out, is that because the system is rectangular it
> shifts and "the ends" com out of the box. the system is comprised of 2
> proteins and 2 peptides.
> the center of the system is essentially where the 15 residues of each of
> the proteins meet.
> autoimage doesn't work as centers the first protein and a big chunk ends up
> outside the box
> centering on all residues almost works, but the tails stick out and the
> whole system ends up turning sideways, so the two edges/ends end up outside
> of the box.
> centering on the 30 core (the 15 from each protein that touch at the center
> of the system) ends up doing the same thing. (system ends up turning
> sideways)
> the axis in order of shortest to longest are x, z, y.
> Is there a way to center on x/2, y/3, z/2?
> I imagine that auto image might work if one could do that. Is there a way
> to specify coordinates to center something on?
> Any thoughts or ideas would be greatly appreciated!
> Thanks,
> Jonathan
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jul 07 2014 - 07:30:02 PDT
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