Re: [AMBER] MMPBSA -O: command not found

From: David A Case <>
Date: Sat, 2 Jul 2016 07:50:23 -0400

On Fri, Jul 01, 2016, Thakur, Abhishek wrote:
> set amber = $AMBERHOME/bin/

> $amber -O -i -o FINAL_RESULTS_MMPBSA.out -sp
> PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> peptide.prmtop -y *.crd
> /projects/lsf_spool/ 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/"

Experiment until you can get this to work -- this is a shell question,
unrelated to Amber.


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Received on Sat Jul 02 2016 - 05:00:03 PDT
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