Sounds to me like a problem with the naming of your S atoms while creating
your inputs in tleap.
I've always seen cysteine sulfurs named SG instead of S1... did you run
your input pdb through pdb4amber before doing the corresponding ZAFF
modifications into the PDB?
Might be another problem.. just a wild guess.
Pedro
El mar, 14 nov 2023 a las 16:25, VERONICA MARTIN HERNANDEZ via AMBER (<
amber.ambermd.org>) escribió:
> 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
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>
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Received on Thu Nov 16 2023 - 07:00:02 PST
