Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial

From: Ross Walker <>
Date: Wed, 29 Jun 2011 02:02:41 -0700

Hi Lee,

When you closed the terminal and opened a new one you probably erased your
setting of the AMBERHOME environment variable. Try:


and see if it is correct. If not then you need to export it again.

export AMBERHOME=/path/to/amber

Then hopefully things should work. You can avoid this step by adding this
export to your ~/.bashrc file so that it gets set for every terminal you

All the best

> -----Original Message-----
> From: Sheau Chen Lee []
> Sent: Tuesday, June 28, 2011 8:23 PM
> To:
> Subject: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
> Hi,
> I'm a beginner in AMBER and i'm using amber9. I accidentally close the
> terminal while i was doing amber advance tutorial for mm-pbsa and LEaP
> does
> not function well after that. Error occurred after the first command
> and
> hence i can't proceed to the next step.
> sclee.sclee-Satellite-L645:~$ > $AMBERHOME/exe/tleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99
> -s: command not found
> sclee.sclee-Satellite-L645:~$ com = loadpdb ras-raf.pdb
> No command 'com' found, but there are 18 similar ones
> com: command not found
> The error did not appear before the terminal closed. May i know what
> shall I
> do?
> Thank you very much.
> Lee.
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Received on Wed Jun 29 2011 - 02:30:03 PDT
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