Dear Dr. Walker,
The machine type should be Athlom i686. And the operating system is Redhat
Linux version 7. I am using Amber 7.
Thanks a lot!
Best,
Jeny
On Thu, 3 Jun 2004, Ross Walker wrote:
> 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
