AmberTools

This is to help document the process to get AmberTools, a set of tools for Assisted Model Building with Energy Refinement (AMBER) into Fedora.

Bundled packages already in Fedora

Fedora package	location in AmberTools	bundled version
arpack	src/arpack	2.1
blas	src/blas	3.0?
boost	src/boost-1.38.0	1.38.0
byacc	src/byacc	20101127
eigen3	src/mtkpp/src/eigen3b2	3.0b2
fftw	src/fftw-3.3	3.3
lapack	src/lapack	3.2
libXmu	src/leap/src/Xmu	20001128
libXpm	src/leap/src/Xpm	3.4
mpi4py	src/mmpbsa_py/mpi4py-1.2.2.tar.gz	1.2.2
netcdf	src/netcdf	3.6.2b6
tinyxml	src/mtkpp/src/tinyxml	2.0 (April 2005)
xblas	src/xblas	1.0 (2005)

Bundled packages which should be fine to put in Fedora

Fedora package	Upstream	Version in AmberTools	Review Request/Status
boost-numeric-bindings	http://beta.boost.org/community/sandbox.html		(not necessary for build)
cifparse	http://sw-tools.pdb.org/apps/CIFPARSE/source.html
libpdb	http://www.cgl.ucsf.edu/Overview/software.html		bundled in ptraj
libpdb++	http://www.cgl.ucsf.edu/Overview/software.html		bundled in reduce
mtkpp	http://mtkpp.martinpeters.ie/	0.2.0
ucpp	http://code.google.com/p/ucpp/	1.3
Wcl	http://search.cpan.org/~jhpb/Wcl-2.7.3/		Old review request

Bundled packages which may be problematic to put in Fedora

Name	Upstream	Version in AmberTools	Status
chamber	AmberTools		non-free license?
libXraw	http://canonical.org/~kragen/Xraw/index.html		non-commercial clause in license
leap	AmberTools		non-free license?
reduce	http://kinemage.biochem.duke.edu/software/reduce.php	3.14.080821	sale restriction?