AMBER Archive (2008)

Subject: Re: AMBER: sleap test failures

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 15 2008 - 17:46:00 CDT

On Tue, Jul 15, 2008, Vlad Cojocaru wrote:
>
> after compiling AmberTools 1.0 I noticed that several sleap test failed.
> However when investigating each failure, it turned out that they were
> not failures. For example, ./sleap/solvate tests appeared as failed all
> but in fact looking at the output and the boxes created, everything
> seemed fine. The diff reported difference between the coordinates of
> .pdb and .pdb.save files but when I loaded these files in vmd they
> overlaid perfectly.
>
> other tests such as the ./sleap/prmtop/Run.prmtop2 failed because of
> loading parm99.dat from different locations when creating box.out and
> box.out.save (in box.out.save there was a strange location of the
> parm99.dat). otherwise the topology files created looked absolutely fine
>
> Is this problem with the sleap tests already known to you ?

As far as I know, we have not seen this before: sleap should be passing all
its tests. So, we will need to know what compiler you used, and more details
about the nature of the reported failures.

There are lots of changes to sleap in version 1.1 of AmberTools, so it might
be worth seeing if those fix your problems.

...dac

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