Dear Amber Users,
I am trying to run a protein-ligand MD simulation and while running the
decomposition of energy via MMGBSA the following error is coming.
Note: I am getting results in MMPBSA and MMGBSA by using the same .prmtop
for complex and receptor and also the .mdcrd, only error I'm getting
while running the decomposition.
This is my decomp.in file where 102 is the ligand and 1-101 is the protein:
#################
input file for running PB and GB
&general
endframe=100000, verbose=1,
interval=2, keep_files=0,
startframe=50000
/
&gb
igb=2, saltcon=0.100,
/
&decomp
idecomp=1, print_res="1-102"
dec_verbose=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.
--------------------------------------------------------------------------
bad atom type: i
File "/apps/scratch/compile/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
app.run_mmpbsa()
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /apps/scratch/compile/amber18/bin/sander failed with prmtop
com_nowat.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
Can you please solve the issue.
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Thu Feb 04 2021 - 22:30:02 PST
