I did it with the help of a friend. Thanks very much!
On Mon, Aug 30, 2010 at 12:21 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The $AMBERHOME/AmberTools/src/antechamber folder is the folder with all of
> the source code used to build the executable. The executable is compiled,
> then moved to $AMBERHOME/bin, so antechamber should be there. However,
> antechamber, during its execution, has the path $AMBERHOME/dat/antechamber
> built into it, which is where it searches for the data files. Therefore,
> only the data files, like CORR_NAME_TYPE.DAT should be in
> $AMBERHOME/dat/antechamber, not antechamber itself.
>
> My guess is that you do not have the proper permissions set on your amber11
> directory. If this is your own, personal machine, you should change the
> ownership of /usr/local/amber11 to your username. You can do this quite
> simply via the command:
>
> sudo chown -R user:user /usr/local/amber11
>
> where "user" is your user name. Then retry your antechamber command. The
> above command executes "change ownership" command recursively over the
> directory, and all subdirectories within, /usr/local/amber11. It changes
> the owner to your username (and the group as well).
>
> Note that a basic working knowledge of UNIX, especially basics of how the
> filesystem is set up and environment variables, will greatly help here.
>
> Good luck!
> Jason
>
> On Mon, Aug 30, 2010 at 11:58 AM, P Bhattacharya <pbhatta.g.clemson.edu
> >wrote:
>
> > My amber11 folder has an AmberTools and a dat folder.
> > Thus, $AmberTools/src/antechamber has no file named CORR_NAME_TYPE.DAT,
> > whereas $dat/antechamber has this file.
> > When I try to run the above command from $dat/antechamber, I get an error
> > "antechamber: command not found
> > ". I am not sure what I should do here. The antechamber folder in dat has
> > no
> > executable files.
> >
> >
> > On Fri, Aug 27, 2010 at 9:34 PM, case <case.biomaps.rutgers.edu> wrote:
> >
> > > On Fri, Aug 27, 2010, P Bhattacharya wrote:
> > > > This is what I have on my screen:
> > > >
> > > >
> > > > Cannot open the CORR_NAME_TYPE.DAT file
> > > > /usr/local/amber11/dat/antechamber/CORR_NAME_TYPE.DAT to read, exit
> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > >
> > > You need to find out if this file (marked above) is present or not; if
> > > you don't know how to do that, maybe a friend can help. If the file is
> > > missing, you will have to re-install AmberTools.
> > >
> > > ...hope this helps....dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Priyanka Bhattacharya
> > PhD candidate
> > Laboratory of Single-Molecule Biophysics and Polymer Physics
> > Department of Physics and Astronomy, Clemson University
> > Lab: Jordan 110
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Priyanka Bhattacharya
PhD candidate
Laboratory of Single-Molecule Biophysics and Polymer Physics
Department of Physics and Astronomy, Clemson University
Lab: Jordan 110
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Received on Mon Aug 30 2010 - 10:30:03 PDT
