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* Remove tri-sulfite bond formation.

Pdbfixer attempts to add di-sulfide bonds to any pair of CYS "S" atoms that are less than 3 A. This procedure fails when multiple such bonds are assigned to a given atom. 

Here we rectify this issue by a greedy algorithm: Atom I is chosen to be bonded to `argmin(distance([:I-1, I])` over all candidate di-sulfide bonds. This procedure will not generally result in a set of minimal distance di-sulfide bonds, but will fix the "tri-sulfide bond" problem. Fixing the more general case would require a solution to global constraint satisfaction problem.

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This patch is provided under the CC0 license (https://creativecommons.org/share-your-work/public-domain/cc0/).
This is not an officially-supported Google product. It is provided ‘as-is’ without any warranty of any kind, whether expressed or implied.

* Update topology.py

Remove a redundant comment.

* Support of Amber FF19SB CMAP

* Update: Support of Amber FF19SB CMAP
Co-authored-by: Kye Won Wang <kyw220@sol.cc.lehigh.edu>

* Use the force group which is assigned to the metadynamics force

* Handle a case when all the force groups are already used

* Fix a typo

Moved _syncWithDisk in init before adding table of biases to CustomCVForce so that loaded biases are included in the biasing potential. (#3052)

* Replaced several AMOEBA bonded forces with custom forces

* Deleted obsolete AMOEBA forces

* Replaced AmoebaPiTorsionForce with custom force

* Update charmmparameterset.py

* Update charmmpsffile.py

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Made ordering of impropers more deterministic

* Fixed typo

* Initial fixes for Apple silicon

Doesn't work yet

* assume vec4 is supported on apple

* Trust the user with env variables

* Fix macos-version-min logic

* Do not alter mass of hydrogens in rigid water

* Do not alter mass of hydrogens in rigid water

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment