Hi
Try adding the following line
source <Path to Amber>/bin/amber.sh or amber.csh (depending on your
environment)
On Tuesday, 30 December 2025, YASHIKA . via AMBER <amber.ambermd.org> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 30 2025 - 04:00:02 PST
