AmberTools
From FedoraProject
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 | ||
| 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? |
