Dear David
Being able to generate the files, but now you are giving this error. Any
idea what it might be?
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/chem/amber18/bin/sander
cpptraj found! Using /usr/local/chem/amber18/bin/cpptraj
Preparing trajectories for simulation...
5000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/chem/amber18/bin/sander
calculating complex contribution...
File "/usr/local/chem/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
app.run_mmpbsa()
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /usr/local/chem/amber18/bin/sander failed with prmtop
complex.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
File "/usr/local/chem/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /usr/local/chem/amber18/bin/sander failed with prmtop
complex.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
File "/usr/local/chem/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/chem/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /usr/local/chem/amber18/bin/sander failed with prmtop
complex.prmtop!
Error occured on rank 3.
Exiting. All files have been retained.
[renato:06551] 1 more process has sent help message help-mpi-api.txt /
mpi-abort
[renato:06551] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
Em ter., 26 de jan. de 2021 às 00:17, David A Case <david.case.rutgers.edu>
escreveu:
> On Mon, Jan 25, 2021, Renato Araujo wrote:
> >
> >I am trying to perform a free energy simulation with the MMPBSA method.
> >
> >Complex natom! = Receiver natom + ligand natom
>
> You need to check your three prmtop files: the number of atoms is the first
> number at the top of these files. Try to figure out why the number of
> atoms
> in the complex doesn't equal the sum of the other two. You may need to
> make
> these prtmop files "by hand", i.e. run tleap yourself for each of the three
> systems.
>
> ....good luck....dac
>
>
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>
--
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Tue Jan 26 2021 - 09:00:02 PST
