[AMBER] MMPBSA -O: command not found

From: Thakur, Abhishek <axt651.miami.edu>
Date: Fri, 1 Jul 2016 19:58:38 +0000


I am trying to calculate MMPBSA calculation with the following script

set amber = $AMBERHOME/bin/MMPBSA.py

# Copy AMBER files to scratch dir

mkdir /scratch/projects/prmt/$user
mkdir /scratch/projects/prmt/$user/$jobname
cd /scratch/projects/prmt/$user/$jobname

#Write input below
cat > mmpbsa.in << EOF
#Input file for running PB

# Execute MMPBSA job serial version
$amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd

But all the time I get an error

/projects/lsf_spool/1467401500.6634518.shell: line 55: -O: command not found

I am using ambertool15 for this calculation.

Kindly help me out to figure it out solution for this.

Thanking you,

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Received on Fri Jul 01 2016 - 13:00:02 PDT
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