Re: [AMBER] Error with cpptraj strip and

From: Jason Swails <>
Date: Mon, 6 Jan 2014 20:50:10 -0500

On Mon, Jan 6, 2014 at 3:46 PM, Daniel Roe <> wrote:

> Hi,
> 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.

This is a good point. As a whole, this idea is more applicable to cpptraj
than it is to ParmEd, since the latter is presumably used to prepare new
topologies for new simulations. The former, on the other hand, is likely
used as often to condense trajectories as it is to prepare topologies for
new simulations.

Perhaps the moral of the store is to use (which uses ParmEd)
to create topologies. ;)

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 06 2014 - 18:00:02 PST
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