Hi everyone
I have calculated MMGBSA for a complex protein ligand of a zinc finger modelled with ZAFF, but I'm running a MMGBSA per residue descomposition and I got the following error:
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/soft/Amber22/amber22/bin/cpptraj
sander found! Using /home/soft/Amber22/amber22/bin/sander
Preparing trajectories for simulation...
1001 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/soft/Amber22/amber22/bin/sander
calculating complex contribution...
bad atom type: S1
bad atom type: S1
bad atom type: S1
bad atom type: S1
bad atom type: S1
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 4.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 2.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 7.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 0.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 3.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
bad atom type: S1
bad atom type: S1
bad atom type: S1
bad atom type: S1
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 8.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 6.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 1.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
bad atom type: S1
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 5.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/soft/Amber22/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/soft/Amber22/amber22/bin/sander failed with prmtop CRBN-LVS-dry.prmtop!
Error occurred on rank 9.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 4 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.
--------------------------------------------------------------------------
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[compute-0-11.local:31548] 9 more processes have sent help message help-mpi-api.txt / mpi-abort
[compute-0-11.local:31548] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
What should I've do?
Thanks in advance
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 14 2023 - 07:30:03 PST
