AMBER Archive (2004)

Subject: Re: AMBER: question about xleap

From: jz7_at_duke.edu
Date: Thu Jun 03 2004 - 13:34:03 CDT

Thanks for all the help!

Yes, the problem seems to be the path and setenv. Now it works. But
another strange thing happens. On the "XLEap: Universe Editor" screen,
all I can see are some strange greek letters. But when I tried to paste
them here, they became the following normal text.

Welcome to LEaP!
Sourcing: /usr/local/AMBER7/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/AMBER7/dat/leap/parm/parm99.dat
Loading library: /usr/local/AMBER7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/AMBER7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/AMBER7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/AMBER7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/AMBER7/dat/leap/lib/ions94.lib
Loading library: /usr/local/AMBER7/dat/leap/lib/solvents.lib

So I am wondering what is wrong with my xleap. Is the front setting not
correct? How can I correct it?

Thanks a lot for your kind help!

Best,
Jeny

On Thu, 3 Jun 2004, Viktor Hornak wrote:

>
> xleap is just a wrapper for xaLeap. In amber8 the wrapper should refer
> to $AMBERHOME/exe/xaLeap (you can look at the file to see what it is
> doing) and therefore should find xaLeap if it found xleap. In previous
> versions of amber you might need to put $AMBERHOME/exe to your $PATH, e.g.:
>
> export PATH="${PATH}:$AMBERHOME/exe"
> (this is for bourne shells; you need to modify for other shells)
>
> Cheers,
> -Viktor
>
> jz7_at_duke.edu wrote:
>
> >Dear all,
> >
> >I am trying to follow the DNA tutorial on Amber website. After setting the
> >path and running nucgen, I cannot load xleap. When I type the command:
> >
> >$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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