9 Commits

Author SHA1 Message Date
Christian Clauss
82703dff73 Fix typos discovered by codespell in Python files (#5173) 2025-12-30 12:21:00 -08:00
João Morado
eaf56f96bc Update AMOEBA XML, .prm files, and parsing of Tinker files (#5086)
* Correct AmoebaAngleTorsion in test_Amoeba18Nucleic of TestForceField

* Update processTinkerForceField to handle latest .prm Tinker files

* Update amoeba2018 XML files

* Update amoeba2013 XML files

* Update amoeba2009 XML files

* Adapt addTorTor to new format in the .prm files

* Fix TorsionTorsion

* Also update the total energy in test_Amoeba18Nucleic

* Update amoebabio18.prm

* Fix nucleic acid test energies

* Correct AmoebaAngleTorsionForce params

* Add new addTorTor to TinkerFiles

* Revert unit fix

* Change to .pdb file which Tinker likes

* Update test_Amoeba18BPTI

* Remove trailing zeros from XML files

* Leave trailing zeros only on 2018 ff

* New element names in 2018

* More digits for surfaceAreaFactor

* More digits for surfaceAreaFactor

* More digits

* Remove debugging print

* Add support to 2009 and 2013 AMOEBA ffs to processTinkerForceField.py

* Add FF specific residues XML files

* Delete old residuesFinal.xml

* Update AMOEBA XML ffs

* Update FFs

* Fix some formatting issues

* Fix "." in scientific notation

* Remove old assertions
2025-10-14 12:55:21 -07:00
Peter Eastman
edee11b601 Fix errors with AMOEBA 2018 (#3311) 2021-11-02 18:33:47 -07:00
Peter Eastman
06767dde49 Added AMOEBA 2018 force field (#3299)
* 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
2021-10-26 09:20:13 -07:00
peastman
69d7dc4fa5 Hopefully finished with supporting nucleotides in AMOEBA 2015-11-19 13:19:48 -08:00
Peter Eastman
fd473eeaff Merge branch 'master' into nucleic 2015-10-29 13:54:00 -07:00
Jason Swails
f7e4653a34 Add a test for AmoebaTorsionTorsionForce that fails because stripUnits doesn't
work for the input variable type.
2015-09-29 00:40:18 -04:00
peastman
0a751b5bd4 Updating scripts to support nucleic acids with AMOEBA 2015-08-18 10:54:45 -07:00
peastman
2781f51864 Added scripts for generating force field XML files 2014-09-02 16:31:03 -07:00