AMBER Archive (2004)

Subject: RE: AMBER: question about xleap

From: Ross Walker (
Date: Thu Jun 03 2004 - 13:03:04 CDT

Hi Jeny,

This seems strange. Xleap is just a script that calls xaleap with the
command $AMBERHOME/exe/xaLeap -I$AMBERHOME/dat/leap/prep
-I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
-I$AMBERHOME/dat/leap/cmd $*

Problems normally occur if your AMBERHOME environment variable is set wrong.
Check that this points to the top level of your amber installation by doing


If this is all ok then the error is very strange. You could try manually
running the xaLeap command with the following lines (assuming you are using
the bash shell):

export XENVIRONENT $AMBERHOME/dat/XaLeap_wcl
$AMBERHOME/exe/xaLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
-I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd -s -f

See if this works. Also try adding the amber exe directory to your path.


If it still doesn't work email me back. If possible include a copy of the
xleap contents (cat xleap) and a directory listing of your amber exe
directory (ls -la)

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

> -----Original Message-----
> From:
> [] On Behalf Of
> Sent: 03 June 2004 10:19
> To:
> Subject: AMBER: question about xleap
> Dear all,
> I am trying to follow the DNA tutorial on Amber website.
> After setting the
> path and running nucgen, I cannot load xleap. When I type the command:
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> It gave the error message:
> xaLeap: Command not found.
> This is very strange. First, the command I use is "xleap",
> not "xaLeap";
> second, I check the directory "$AMBERHOME/exe/", both xleap
> and xaLeap are
> there. So what is the problem?
> Thanks a lot for your kind help!
> Best,
> Jeny
> --------------------------------------------------------------
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