GitLab

* fix formal charge reading and writing in pdb files; store formal charge in topology

* use formalCharge in public api

* permissive reading

* fix writing

* fix

* add test for formal charges

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Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: Jason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

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Co-authored-by: Jason Swails <jason@entos.ai>

* Add benchmarks from Amber20 benchmark suite to standard benchmark script

* Add ensemble option; don't change hydrogen mass in amber input files

* Download and extract .tar.gz using pure python code, no wget/tar dependencies

* Rename amber tests

* add opc and opc3 models

* update to match https://bioinformatics.cs.vt.edu/~izadi/OPC_Gromacs/opc.top



* opc box, converted from ambertools-22.0-py38h6177452_1/dat/leap/lib/opcbox.off

* change values to make serialized system match one created from prmtop as close as possible

* unit test for opc water

* opc - final values, match frcmod.opc; derivation in comments

* opc3 water - final values, shows derivation

* opc3box made from ambertools 22 dat/leap/lib/opc3box.off

* add opc3 water test

* add opc and opc3 to docs

* move tests to TestForceField.py

* move opc tests out of amoeba tests, oops

* move opcbox and opc3box pdb files
Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* Do not add constraints involving extra particles

* Added test case

* Access atom element field

* Update GB-Neck2 force regression test

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests

* Improved handling of atoms with alternate locations

* Fixed a test failure caused by an invalid PDB file

* Support of Amber FF19SB CMAP

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

* 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

* Implementation of OPLS through DMS reader

* Improved Implementation of OPLS through DMS reader

* raise errors for invalid implicit solvent settings

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

Changed format to 'pdbx' for consistency within the test framework. Added 'cif' to CMakeLists.txt for correctness for the future

I’m not sure how to trigger the unit testing suite, but this code
should test the changes I’ve made.