Dear Support Team,
I am running MMGBSA analysis on the BRaF (C-DAC) cluster using the
centrally installed Amber16. I am submitting the job using the standard
MMPBSA input script (MMGBSA with &general, &gb, &pb and &decomp sections).
However, the job fails immediately with a Python traceback error before
reading the input script.
Below are the details of the job submission and the error.
Input sh script
#!/bin/sh
#SBATCH -N 1
#SBATCH --ntasks-per-node=16
#SBATCH --job-name=m2
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out
#SBATCH --partition=braf
#SBATCH --export=ALL
# Load the Intel toolchain
ml intel/2018_4
# Set OMP threads, if your application is multithreaded
# OMP_NUM_THREADS=$SLURM_NTASKS #Optional, uncomment this line if required.
mpirun -n 16 /home/apps/amber16_intel/bin/MMPBSA.py.MPI -O -i
mmpbsa_per-residue.in -cp complex_m2_nosolvent.parm7 -rp protein_wt.parm7
-lp sirna_wt.parm7 -y combined_wt.mdcrd -o result_m4_per-residue.dat
Error file contain
Traceback (most recent call last):
File "/home/apps/amber16_intel/bin/MMPBSA.py.MPI", line 48, in <module>
Traceback (most recent call last):
I would like to know how this issue can be resolved on the cluster. Could
anyone please advise or help in solving this.
With regards
Yashika
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Received on Tue Dec 30 2025 - 02:30:02 PST
