CPPTRAJ: Trajectory analysis based on Ptraj, written in C++.
Daniel R. Roe 2010

CPPTRAJ by default will be installed as part of AmberTools. CPPTRAJ can also
be installed as a stand-alone program. The configure script in this directory
is for stand-alone compilation only.

'./configure gnu' should be adequate to set up compilation for most systems.

Run './configure --help' for list of configure options. 

The configure script by default sets everything up to link dynamically. If you 
encounter linking errors you may need to specify library locations using the
'--with-LIB=' options. For example, to use Netcdf compiled with Amber use the
option:

--with-netcdf=$AMBERHOME/AmberTools/src/netcdf

Alternatively, individual libraries can be disabled with the '-noLIB' options.

After config.h has been successfully generated, 'make install' will
compile and place the cpptraj binary in the ./bin/ directory.

To test the binary in the ./bin/ directory either run 'make check' or change 
to the 'test' directory and run 'make test'. If testing the stand-alone
version the environment variable CPPTRAJHOME should be set to this directory
and AMBERHOME should be unset (otherwise the binary in AMBERHOME/bin will
be used for testing).

