[Viswanath Vittaladevaram]

Hi,

I tried as much as I could for MM-PBSA calculations using this script and found the following error.

Script:

#!/bin/sh

#SBATCH --job-name=fnIII-12_SAM-EA10_MMPBSA             

#SBATCH -A ngche132c 

#SBATCH -N 1

#SBATCH -t 24:00:00

module purge

module load amber/18

module load intel/2017u8

module load gcc/8.2.0

cd $SLURM_SUBMIT_DIR

source /ichec/packages/amber/18/amber.sh

export DO_PARALLEL="mpirun -np 40 MMPBSA.py.MPI"

for X in 1 2 3 4 5 6 7

do

    cd pbsa_${X}

    $DO_PARALLEL -O -i pbsa.in -cp ../protein-surface.parm7 -lp ../protein.parm7 -rp ../surface.parm7 -y ../fnIII-12-14_SAM-EA10_T300-nw.nc -o FINAL_RESULTS_MMPBSA_${X}.dat -do FINAL_DECOMP_MMPBSA_${X}.dat > pbsa.log_${X}warnings.warn('ligand_mask overwritten with default\n')

Warning:

/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py:606: UserWarning: ligand_mask overwritten with default

  warnings.warn('ligand_mask overwritten with default\n')

/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py:606: UserWarning: ligand_mask overwritten with default

  warnings.warn('ligand_mask overwritten with default\n')

  File "/ichec/packages/amber/18/bin/MMPBSA.py.MPI", line 99, in <module>

    app.file_setup()

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup

    self.mpi_size, str(external_progs['cpptraj']), self.pre)

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 76, in make_trajectories

    raise MMPBSA_Error('Must have at least as many frames as processors!')

MMPBSA_Error: Must have at least as many frames as processors!

Error occured on rank 0.

Exiting. All files have been retained.

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBS

Anyone can help on this,

Regards,