Try trashing the AmberTools python and just use the system Python (you can
pass -nopython to the configure script to suppress building an
Amber-bundled python).
Alternatively, you can manually edit the shebang (#!) line of the
AT15_Amber11.py script to use a specific python (e.g. /usr/bin/python)
rather than /usr/bin/env python (which just pulls the first one from the
PATH). Then you can try running AT15_Amber11.py again.
HTH,
Jason
On Wed, Mar 21, 2012 at 7:57 AM, Adam Jion <adamjion.yahoo.com> wrote:
> Hi!
>
> I'm having problems compiling Amber 11 on my 64-bit Ubuntu machine (all
> the patches for AmberTools 1.5 and Amber 11 have been applied)
>
> The official error I get is:
> cp: cannot stat `../../AmberTools/src/netcdf/include/*.mod': No such file
> or directory
> make[1]: *** [netcdf.mod] Error 1
> make[1]: Leaving directory `/home/adam/amber11/src/sander'
> make: *** [serial] Error 2
>
>
> But I suspect its due to a bad implementation of AT15_Amber11.py by
> AmberTools's Python which led to the following error when compiling
> AmberTools:
>
> "Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> ImportError: No module named site"
>
> So how do I fix my problems?
>
> Appreciate any help,
> Adam
>
> ps. I also have a (negligible?) error of "Could not find the X11
> libraries; you may need to edit config.h
> to set the XHOME and XLIBS variables" when configuring AmberTools.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 21 2012 - 05:30:05 PDT
