Re: [AMBER] Error with cpptraj strip and

From: Daniel Roe <>
Date: Mon, 6 Jan 2014 13:46:14 -0700


On Mon, Jan 6, 2014 at 1:28 PM, Brian Radak <> wrote:

> I don't know what, if any, part of this is a bug. Presumably a stripped
> trajectory should always have IFBOX = 0?

No, in many cases you may want to preserve unit cell information. This
allows you e.g. to re-image in the future if you want (centering on a
different part of the molecule) etc. Once you remove the box information
you're stuck with the trajectory as-is.

You can prevent box information from being written to a trajectory if you
want with the 'nobox' keyword for the trajout/outtraj commands. You can
also remove box information with 'box nobox' (for trajectory processing) or
'parmbox nobox' (to modify box info in the topology itself).

Hope this helps,


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 Jan 06 2014 - 13:00:04 PST
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