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

From: David A Case <>
Date: Thu, 30 Jun 2011 08:29:31 -0400

On Thu, Jun 30, 2011, Sheau Chen Lee wrote:

> > > sclee.sclee-Satellite-L645:~$ > $AMBERHOME/exe/tleap -s -f
> > > $AMBERHOME/dat/leap/cmd/leaprc.ff99
> > > -s: command not found

This is hard to parse, but you need to try some experiments. I'm assuming
that the first two lines were originally on the same line. But even in
AMBERHOME were not set correctly, I don't quite see why you would not receive
an error like "/exe/tleap: command not found".

So, try some combination like this:

which tleap (to ensure that your PATH is correct)
tleap -f leaprc.ff99SB (to see if you can get things started)

Note that in current versions of Amber, the leaprc.ff99 has been moved to the
"oldff" subdirectory, and hence the above command would not work anyway. You
should *not* be using ff99 unless you really know what you are doing, i.e.
that you understand that this is an obsolete force field that is not
recommended for general use.


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Received on Thu Jun 30 2011 - 05:30:07 PDT
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