After changing the mmpbsa.in into:
input file for running PB and GB
&general
endframe=125000, verbose=1, keep_files=2, interval=25,
strip_mask=":WAT:Cl-:Na+",
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100, inp=1, radiopt=0
/
I got:
File "/software/local/el6/AMD/amber14-python2.7.5/bin/MMPBSA.py.MPI",
line 104, in <module>
app.run_mmpbsa()
File
"/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError:
/software/local/el6/AMD/amber14-python2.7.5/bin/mmpbsa_py_energy failed
with prmtop complex.prmtop!
PB bomb in pb_setgrd(): Allocation aborted
Is is consistent with having run out of memory?
best regards
Urszula
> Dear amber users,
>
> After running mmpbsa.py I am getting an error message:
>
>
> [n1073-amd.zeus:50924] 1 more process has sent help message
> help-mpi-runtime.txt / mpi_init:warn-fork
> [n1073-amd.zeus:50924] Set MCA parameter "orte_base_help_aggregate" to 0
> to see all help / error messages
> [n1073-amd.zeus:50924] 8 more processes have sent help message
> help-mpi-runtime.txt / mpi_init:warn-fork
> File "/software/local/el6/AMD/amber14-python2.7.5/bin/MMPBSA.py.MPI",
> line 104, in <module>
> app.run_mmpbsa()
> File
> "/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/software/local/el6/AMD/amber14-python2.7.5/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 431, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError:
> /software/local/el6/AMD/amber14-python2.7.5/bin/mmpbsa_py_energy failed
> with prmtop complex.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom 4675 C5'
> CI
>
> What did go wrong here?
>
> The prmtop files I generated by running ante-mmpbsa.py:
>
> ante-MMPBSA.py -p solvated_complex.prmtop -c complex.prmtop -r
> receptor.prmtop -l ligand.prmtop -n :286-331 --radii=mbondi2 -s
> :Cl-,:WAT,Na+
>
>
> the mmpbsa.in input file is:
>
> input file for running PB and GB
> &general
> endframe=125000, verbose=1, keep_files=2, interval=25,
> strip_mask=":WAT:Cl-:Na+",
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
>
> thanks in advance for any help
>
> best regards
> Urszula Uciechowska
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Mon Aug 17 2015 - 02:30:05 PDT
