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parameters to a ProteinStructure before calling createSystem.

really used CMake in-depth before).

Hopefully this fixes the Travis-CI build failures.

(again, code pulled from ParmEd) and update the tests to include this.

pick up some bugs that were not caught in my initial test following the port
from ParmEd.

All 4 tests pass right now, although no periodic systems are being tested.
Currently CHARMM, XPLOR, and VMD tests are all being run (for the same ala-3
system).

Disable implicit solvent tests, since there is no robust radii assignment
routine yet (the radii are stored in the Amber topology file).  I will port my
assignment routine from ParmEd here shortly and then re-enable the GB tests.

correct list of modules (the existing list was for the ParmEd implementation
which separated out the OpenMM integration so not having it was not fatal).

Add a test case and example for running with CHARMM files.

Currently gives exactly the same energy as the same files passed through chamber
(which, in turn, was validated to machine precision against CHARMM itself).

A previous commit had changed OpenMM_headers.i to OpenMMSwigHeaders.i without changing the corresponding include statement in OpenMM.i.

from all .cpp and .h files.

Install SWIG interface definition to the include directory, so outside plugins can use it when building their Python APIs

Added step limit for LocalEnergyMinimizer in Modeller.addHydrogens() to prevent hangs with bad structures.