Hello,
AMBERHOME is an environment variable needed for some programs to operate.
Amber typically requires a general working knowledge of Unix to use, and
solving this problem requires such knowledge.
See the following website: http://www.ee.surrey.ac.uk/Teaching/Unix/ , which
provides a good overview on Unix functionality. Chapter 8 has a section on
environment variables, but a general working knowledge of most sections will
greatly help you in the future if you plan to use Amber (or any other
command-line-based unix program) with any kind of regularity.
As has already been pointed out, there are a couple ways of setting
environment variables based on which shell you are using (if you don't know
what that means, it, too, is explained in the above website I believe).
export AMBERHOME=/path/to/amber11
or
setenv AMBERHOME "/path/to/amber11"
However, the "/path/to/amber11" is dependent on your system, so using either
of the above commands verbatim will not work. Since we don't know where
you've placed amber11 (or amber10, or any other version), we have know way
of knowing what "/path/to/" should really be. Again, this requires a
general working knowledge of Unix obtained by committing a modest amount of
time to the above tutorial.
I'm sorry if I've oversimplified things here, but based on your email, I
don't know what level of experience you have with Unix operating systems,
and I figured it was better to err on the side of too little so my advice
won't be too technical. If you know someone that has a good knowledge of
Unix that is willing to work with you, they may be valuable resources to
help.
Hope this helps,
Jason
On Wed, Jun 23, 2010 at 5:07 PM, Ping <xiuchen.iastate.edu> wrote:
> On Wed, Jun 23, 2010 at 4:05 PM, jane <jane.chen.1016.gmail.com> wrote:
>
> > Hi Heather,
> >
> > Thanks for your reply. But the message still shows that it is not set
> after
> > I typed in that command.
> >
> > [xiuchen.sw2123-06 ~/Desktop]$ setenv
> > AMBERHOME/home/xiuchen/Desktop/amber11
> > [xiuchen.sw2123-06 ~/Desktop]$
> > /home/xiuchen/Desktop/amber11/bin/antechamber -i HSA-1E78_h.pdb -fi pdb
> -o
> > HSA-1E78.mol2 -fo mol2 -c bcc -s 2
> > AMBERHOME is not set!
> > [xiuchen.sw2123-06 ~/Desktop]$ cd amber11
> > [xiuchen.sw2123-06 amber11]$ cd bin
> > [xiuchen.sw2123-06 bin]$ /home/xiuchen/Desktop/amber11/bin/antechamber
> -i
> > HSA-1E78_h.pdb -fi pdb -o HSA-1E78.mol2 -fo mol2 -c bcc -s 2
> > AMBERHOME is not set!
> > [xiuchen.sw2123-06 bin]$
> >
> > Thanks,
> > Ping
> >
> >
> >
> > On Wed, Jun 23, 2010 at 3:45 PM, Heather Condurso <condurso.bc.edu>
> wrote:
> >
> >> setenv AMBERHOME /(path to amber)
> >>
> >>
> >> | On Wed, 23 Jun 2010 15:42:06 -0500
> >> | Ping <xiuchen.iastate.edu> wrote:
> >> | Hi all,
> >> |
> >> | When I am using the antechamber command, a message shows that "
> >> AMBERHOME is
> >> | not set". Does anyone know how to fix this problem?
> >> |
> >> | Thank you very much!
> >> |
> >> | Ping
> >> | _______________________________________________
> >> | AMBER mailing list
> >> | AMBER.ambermd.org
> >> | http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 23 2010 - 14:30:04 PDT
