Dear Jeny,
This sounds to me like you may be missing the font that xleap uses. What
machine type and operating system are you running? And what version of
Amber?
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of jz7.duke.edu
> Sent: 03 June 2004 11:34
> To: amber.scripps.edu
> Subject: Re: AMBER: question about xleap
>
> 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}:$AMBERHOME/exe"
> > (this is for bourne shells; you need to modify for other shells)
> >
> > Cheers,
> > -Viktor
> >
> > jz7.duke.edu wrote:
> >
> > >Dear all,
> > >
> > >I am trying to follow the DNA tutorial on Amber website.
> After setting the
> > >path and running nucgen, I cannot load xleap. When I type
> the command:
> > >
> > >$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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Received on Thu Jun 03 2004 - 20:53:01 PDT
