Hi David
I tried running non-parallel on similar system. This time getting new error
Loading and checking parameter files for compatibility...
File "/opt/amber/amber14/bin/MMPBSA.py", line 102, in <module>
app.loadcheck_prmtops()
File
"/opt/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/opt/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/readparm.py",
line 69, in LoadParm
parm = parm.view(AmberParm)
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/amberformat.py",
line 411, in view
return cls.load_from_rawdata(self)
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py",
line 240, in load_from_rawdata
inst.initialize_topology()
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py",
line 196, in initialize_topology
self.load_structure()
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py",
line 384, in load_structure
self._check_section_lengths()
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py",
line 1215, in _check_section_lengths
check_length('ATOMIC_NUMBER', natom, False)
File
"/opt/amber/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py",
line 1204, in check_length
(key, len(self.parm_data[key]), length))
AmberParmError: FLAG ATOMIC_NUMBER has 73052 elements; expected 7940
Exiting. All files have been retained.
Please help
Best Regards
On Mon, Apr 24, 2017 at 7:55 PM, David Case <david.case.rutgers.edu> wrote:
> On Mon, Apr 24, 2017, Vertika Gautam wrote:
> >
> > I am performing 3drism (first time) for energy calculation of a
> > protein-protein system.
> >
> > mpirun -np 32 MMPBSA.py.MPI -O -i mmpbsa-rism.in -o
> > FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp t.top -cp
> > enz-lig.top -rp enz.top -lp lig.top -y c96-100.mdcrd > progress.log
> 2>&1
>
> OK: if this is not working, try a non-parallel run on a single frame. Look
> in the output files for indications of an error.
>
> > CalcError: /opt/amber/amber14/bin/rism3d.snglpnt failed with prmtop
> lig.top!
> > Error occured on rank 29.
> > Exiting. All files have been retained.
>
> You should have the rism3d.snglpnt output files available. But it helps to
> reduce confusion and help debugging if you run MMPBSA.py instead of
> MMPBSA.py.MPI.
>
> ....dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vertika Gautam
Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya
*e-mail address: vartikapisces.gmail.com
<vartikapisces.gmail.com>
vartikapisces.hotmail.com <vartikapisces.hotmail.com>
01112294191*
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Received on Sat May 20 2017 - 14:00:03 PDT
