Dear Amber Mailing List,
I have a ligand containing Iodine, and I am attempting to run mmgbsa on the trajectory. I am experiencing a 'bad atom type: i' error, whether I use igb=2 or igb=5 (started out with igb=5 as the production was done using mbondi2). I am running this using the mmpbsa.py.MPI from AMBER19 and running it as a job on a computing cluster. I have seen that some others have had this error before, http://archive.ambermd.org/201909/0086.html ; http://archive.ambermd.org/201104/0099.html but I can't seem to get it working. Has iodine been parameterized yet?
The mmpbsa.in I am using:
#Calculating energy with nmode and residue decomposition
&general
verbose=1, startframe=1, interval=5, verbose=2,
#entropy=1
/
&gb
igb=5, saltcon=0.15,
/
&decomp
idecomp=2, dec_verbose=3,
/
I am running the mmgbsa job with the following command:
mpirun -np 40 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS_MMPBSA.dat -cp complex.prmtop \
-rp receptor.prmtop -lp ligand.prmtop -y *.netcdf -do DECMP_MMPBSA.dat \
-deo decomp_energy.csv > progress.log
This is the error I am experiencing:
[cl5n044:68915] 39 more processes have sent help message help-mpi-btl-openib.txt / no device params found
[cl5n044:68915] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[cl5n044:68915] 39 more processes have sent help message help-mpi-btl-openib.txt / error in device init
bad atom type: i
bad atom type: i
bad atom type: i
bad atom type: i
bad atom type: i
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/MMPBSA.py.MPI", line 100, in <module>
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/MMPBSA.py.MPI", line 100, in <module>
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/MMPBSA.py.MPI", line 100, in <module>
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 0.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 7.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /pkg/suse12/software/Amber/18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 6.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
Any help or guidance would be greatly appreciated.
Thanks in advance,
Zach
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Received on Tue Feb 07 2023 - 00:30:03 PST
