AMBER Archive (2008)

Subject: Re: AMBER: sleap test failures

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Jul 16 2008 - 03:07:48 CDT

Hi David,

I used icc, probably I should have used gcc for amber tools. But I tried
to compile everything with one compiler suite.
Before I give details, let me try the 1.1 version and if I still get
those failures, I'll come back.

Best
vlad

David A. Case wrote:
> 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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Dr. Vlad Cojocaru

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e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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