Custom Search
---
> -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/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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Received on Sun Jul 20 2008 - 06:07:09 PDT