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
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Received on Mon Aug 30 2010 - 09:30:06 PDT
