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 - 07:40:12 CDT

Dear David, ambers,

The sleap tests passed correctly with AmberTools 1.1 (compiled again
with icc -- "./configure_at icc ; make -f Makefile_at""). Only one test
seemed to fail in antechamber/sustiva (./Run.sustiva). But this again
run correctly although it appears to have failed. Below is the message
from make test, the diff file and the .out file. As you may notice the
leap.out file looks absolutely fine. However, the diff writes strangely
"/scratch/nodE-6-01" instead of "scratch/node-06-01" (which is correct
in leap.out). In leap.out.save these lines point to /home/case/amber10 ....

The sleap tests that I reported in my previous email appeared to fail in
a very similar way in AmberTools 1.0

Best wishes
vlad

-------------------message from make test
----------------------------------------
-------------------message from make test
----------------------------------------
diffing leap.out.save with leap.out
possible FAILURE: check leap.out.dif

-------------------leap.out.dif------------------------------------------------------
-------------------leap.out.dif------------------------------------------------------
1,4c1,4
< -I: Adding dat/leap/prep to search path.
< -I: Adding dat/leap/lib to search path.
< -I: Adding dat/leap/parm to search path.
< -I: Adding dat/leap/cmd to search path. 

---
 > -I: Adding 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/prep 
to search path.
 > -I: Adding 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/lib 
to search path.
 > -I: Adding 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/parm 
to search path.
 > -I: Adding 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd 
to search path.
9,10c9,10
< ----- Source: dat/leap/cmd/leaprc.gaff
< ----- Source of dat/leap/cmd/leaprc.gaff done
---
 > ----- Source: 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd/leaprc.gaff
 > ----- Source of 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd/leaprc.gaff 
done
12c12
< Loading parameters: dat/leap/parm/gaff.dat
---
 > Loading parameters: 
/scratch/nodE-6-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/parm/gaff.dat

---------------------------------leap.out--------------------------------------------------
---------------------------------leap.out--------------------------------------------------
-I: Adding 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/prep 
to search path.
-I: Adding 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/lib 
to search path.
-I: Adding 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/parm 
to search path.
-I: Adding 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd 
to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.in.

Welcome to LEaP!
Sourcing: ./leap.in
----- Source: 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd/leaprc.gaff
----- Source of 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/cmd/leaprc.gaff 
done
Log file: ./leap.log
Loading parameters: 
/scratch/node-06-01/cojocavd/Software/amber10_intel_mpich2/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 
2003)
Loading parameters: ./frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./sustiva.mol2
Reading MOLECULE named SUS
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 7 12 duplicates bond ('triangular' bond) or angle ('square' bond)

1-4: angle 7 9 duplicates bond ('triangular' bond) or angle ('square' bond)

1-4: angle 9 12 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
 total 8 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res     total affected

        SUS     1
  )
 (no restraints)
        Quit

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

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

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

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

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