AMBER Archive (2008)

Subject: Re: AMBER: Problem with box dimension in AmberTools ptraj

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Jul 22 2008 - 11:47:42 CDT

> I was having trouble imaging with the latest version of ptraj found in the
> AmberTools 1.0 package. I noticed that the archives have several other
> instances in the past few months of problems with imaging, but it didn't
> seem like there was any resolution to these problems.
...
> In my investigations into the weirdness of the imaging, I came across what
> might be the issue. It seems to me that if you read in an Amber coordinate
> file with box information and write out a new one, the box dimensions are
> altered upon output. As a test case of this, I have a 50-frame MD

AmberTools 1.2 should fix this; I messed up when adding in support for the
new replica-exchange format and this lead to box size errors. Should be
OK with the newer version of ptraj in AmberTools 1.2.

--tom

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