Dear Amber Users
when I try to run the program directly with this command it ran
$AMBERHOME/bin/MMPBSA.py -O -i energy.in -o FINAL_RESULTS_MMPBSA.dat -eo
MMPBSA.PER-FRAME.dat -sp wet.complex.prmtop -srp wet.rec.prmtop
-slp wet.lig.prmtop -cp gas.complex.prmtop -rp gas.receptor.prmtop -lp
gas.ligand.prmtop -y md1.mdcrd -yr md1-rec.mdcrd -yl md1-lig.mdcrd
but when I try to run it through the script
#!/bin/sh
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -j y
#$ -r y
#$ -N md
#$ -o LOGFILES_energy_O
#$ -e LOGFILES_energy_E
#### #$ -pe amber 42
#$ -pe amber 1
export AMBERHOME=/usr/local/bio/amber20
echo "THIS IS THE VAR="
echo $AMBERHOME
echo "VALUE"
$AMBERHOME/bin/MMPBSA.py -O -i energy.in -o FINAL_RESULTS_MMPBSA.dat -eo
MMPBSA.PER-FRAME.dat -sp wet.complex.prmtop -srp wet.rec.prmtop
-slp wet.lig.prmtop -cp gas.complex.prmtop -rp gas.receptor.prmtop -lp
gas.ligand.prmtop -y md1.mdcrd -yr md1-rec.mdcrd -yl md1-lig.mdcrd
it gives me the error
Unable to read script file because of error: invalid option argument "-O".
Kindly guide me is this error. I ran MMPBSA several time but this is the
first time I am facing this error, Is this because of HPC or what kind of
error is this.
Best
Rehan
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Received on Sat Oct 30 2021 - 16:00:02 PDT
