[AMBER] imaging problem

From: Jonathan Gough <jonathan.d.gough.gmail.com>
Date: Sun, 6 Jul 2014 17:41:48 -0400

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

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!

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Received on Sun Jul 06 2014 - 15:00:03 PDT
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