AmberTools

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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)
ucpp src/ucpp-1.3 1.3
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
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?