Does below give you any output?
$AMBERHOME/bin/MMPBSA.py -O
You should expect to see
InputError: No input file was provided!
Enter `MMPBSA.py --help` for help
If not, you should check if you have $AMBERHOME/bin/MMPBSA.py
Hai
On Fri, Jul 1, 2016 at 3:58 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> 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
> &general
> verbose=2,
> /
> &pb
> istrng=0.100,
> /
> EOF
>
> # 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,
>
> AT
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 01 2016 - 13:30:03 PDT
