On Fri, Jul 01, 2016, Thakur, Abhishek wrote:
>
> set amber = $AMBERHOME/bin/MMPBSA.py
> $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
>
> /projects/lsf_spool/1467401500.6634518.shell: line 55: -O: command not found
This means that the $amber variable is expanded to an empty string.
Add "echo $amber" after the set command to see what you are getting.
Your syntax is csh syntax: is that the shell you are using? If you are using
sh/bash/zsh you should write "amber=$AMBERHOME/bin/MMPBSA.py"
Experiment until you can get this to work -- this is a shell question,
unrelated to Amber.
....dac
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Received on Sat Jul 02 2016 - 05:00:03 PDT
