Release notes from ParmEd

ParmEd v4.3.1

2026-01-12T14:20:20Z

What's Changed

Update dev environment and add testing for python 3.13 by @chrisjonesBSU in #1391
Resolve issue/1386, fix numpy.compat deprecation warning by @MattBurn in #1387

New Contributors

@chrisjonesBSU made their first contribution in #1391
@MattBurn made their first contribution in #1387

Full Changelog: 4.3.0...4.4.0

ParmEd v4.3.0

2024-10-30T16:54:23Z

What's Changed

Fixed Improper Method Call: Replaced mktemp by @fazledyn-or in #1328
Add support for 12-6-4 models. by @swails in #1346
Fix wildcard sorting when writing Amber parameter sets (fixes #1347) by @murfalo in #1348
Match tleap by ensuring parm{10|99|15}.dat are loaded no more than once by @murfalo in #1353
Ignore TURN comments in PDBs by @slochower in #1351
fix SyntaxWarning: invalid escape sequence by @njzjz in #1350
Fix output of changeLJSingleType by @swails in #1355
Bugfixed AtomType equality operator by @murfalo in #1360
Fix the build wrt RDKit package issues by @swails in #1370
Fixed compatibility with NumPy 2.0+ by @vedranmiletic in #1374
Fix serialization of structure with bond type attributes and add test by @swails in #1376
Ensure PBC box vectors are in reduced form for OpenMM by @nffaruk in #1368
Improve mdin parsing to not split restraintmask fields using '=' wildcard char by @nffaruk in #1369
Fix velocity unit scale for existing vels passed to OpenMM by @nffaruk in #1367
Switch to non-deprecated miniforge by @swails in #1378

New Contributors

@fazledyn-or made their first contribution in #1328
@murfalo made their first contribution in #1348
@slochower made their first contribution in #1351
@vedranmiletic made their first contribution in #1374

Full Changelog: 4.2.2...4.3.0

ParmEd v4.2.2

2023-10-24T13:50:21Z

What's Changed

Fix setup.py by @swails in #1327

Full Changelog: 4.2.1...4.2.2

ParmEd v4.2.1

2023-10-24T08:20:38Z

What's Changed

Support Python 3.12 by @mattwthompson in #1325
Fix usage of lru_cache for cache in py38 by @swails in #1326

Full Changelog: 4.2.0...4.2.1

ParmEd v4.2.0

2023-10-23T14:24:37Z

What's Changed

Added 3D-RISM and GBNSR6 to mdin configuration by @Valdes-Tresanco-MS in #1305
Basic routines for internal to cartesian coordinate conversion by @bradakta in #1311
Transfer chain IDs to OpenMM topology. by @jpthompson17 in #1310
Add a library of all CCD residues separate from modified amino/nucleic acids by @swails in #1315
Fix Python 3.8 support by @swails in #1319
Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions by @jpthompson17 in #1316

New Contributors

@bradakta made their first contribution in #1311

Full Changelog: 4.1.0...4.2.0

ParmEd v4.1.0

2023-04-07T13:55:39Z

What's Changed

set python_requires to >=3.8 by @njzjz in #1285
switch out copy with deepcopy for structure.copy() method by @daico007 in #1290
Drude psf where NUMANISO is zero by @florianjoerg in #1274
lonepair refinement by @JohannesKarwou in #1266
Set atomic number when applying a patch by @peastman in #1275
Prefer patch versions that replace external bonds by @peastman in #1278
Enable changing C4 terms in LJ pairs individually by @KevinMei-Github in #1277
Fix an error with mdin changing by @swails in #1299
Fix bug with adding positional restraints for OpenMM (#1301) by @nffaruk in #1302
Fix bug with restart reporter for OpenMM minimization by @nffaruk in #1303
Preserve formal charges from PDB and CIF files if present over templates by @swails in #1304

New Contributors

@njzjz made their first contribution in #1285
@daico007 made their first contribution in #1290
@florianjoerg made their first contribution in #1274
@JohannesKarwou made their first contribution in #1266
@KevinMei-Github made their first contribution in #1277
@nffaruk made their first contribution in #1302

Full Changelog: 4.0.0...4.1.0

ParmEd v4.0.0

2023-01-27T17:56:47Z

This is a major ParmEd release with some minor backwards-incompatible changes:

Python support has been restricted to Python v3.8 and newer (dropping support for Python 2.7)
Support OpenMM 7.5 and older has been dropped. The OpenMM integration will now require OpenMM 7.6 or newer.
The xparmed GUI has been removed

What's Changed

Check to make sure CHARMM patch doesn't create empty residue by @jchodera in #1139
Major cleanup and remove Python 2 support by @swails in #1138
Bug in Atom.umass by @anabiman in #1141
Remove duplicate definition by @swails in #1144
Add Entos converters and add support for LJ-PME in OpenMM by @swails in #1145
Add DL poly writers by @swails in #1146
Add citation for ParmEd to README by @swails in #1147
Add atomic number guessing based on mass for PSF files. by @swails in #802
Add some tests for the checkValidity command by @swails in #1148
Fix a bug where parm.save() would convert to a ChamberParm if CMAPs were present, even though Amber has CMAPs now by @swails in #1152
fix wrong dim in box estimation by @anabiman in #1165
Improving parameterized inference by @anabiman in #1162
missing check for DihedralType in Dihedral.funct by @anabiman in #1170
Add explicit hydrogens when loading in SMILES by @justinGilmer in #1172
Fix/openmm namespace change by @mikemhenry in #1176
Allow some 1-4 interactions to be unscaled by @peastman in #1149
Bump recursion limit by @swails in #1180
Base unscaled pairs on all atoms in a torsion by @peastman in #1182
Prototype for heterogenous mass repartitioning by @bradakstx in #1186
Perceive external bonds (necessary for glycam ffxml conversion) by @zhang-ivy in #1184
nbfix_symmetry - gromacs test skip by @tjwatson-stx in #1196
Fix issue with colliding atom types in structure addition by @swails in #1199
Try to fix osx builds more permanently by @swails in #1200
Converted AMOEBA code to work with OpenMM 7.6 by @peastman in #1201
reading gromacs topologies with insertion codes fixed by @Valdes-Tresanco-MS in #1219
Reading a Gromacs topology fails with insertion code or negative number by @Valdes-Tresanco-MS in #1225
PBRadii by @Valdes-Tresanco-MS in #1230
Fix energy printout by @swails in #1232
Fix AmberParm.from_structure with CMAPs by @swails in #1233
Add support for more CHARMM force fields by @swails in #1157
Add an RDKit export utility by @swails in #1252
Fix bond order assignment in structure copying and slicing by @swails in #1256
Ignore blank lines in mol2 by @adw62 in #1263
Delete test_parmed_visualization.py by @swails in #1269
Fix bug reported by Alex Sodt by @swails in #1281
Improve CIF and PDB parsing and add informatics fields to Atom and Bond by @swails in #1284

New Contributors

@anabiman made their first contribution in #1141
@justinGilmer made their first contribution in #1172
@mikemhenry made their first contribution in #1176
@bradakstx made their first contribution in #1186
@zhang-ivy made their first contribution in #1184
@tjwatson-stx made their first contribution in #1196
@adw62 made their first contribution in #1263

Full Changelog: 3.4.0...4.0.0

ParmEd v3.4.4

2023-01-17T03:21:20Z

Bugs fixed

reading gromacs topologies with insertion codes fixed by @Valdes-Tresanco-MS in #1220
Do not force CMAPs to write a ChamberParm instance by @swails in #1224
Reading a Gromacs topology fails with insertion code or negative number by @Valdes-Tresanco-MS in #1222
New pb radii sets by @Valdes-Tresanco-MS in #1227
Fix AmberParm.from_structure with CMAPs v3.4 by @swails in #1234
Added 3D-RISM with sander to mdin by @Valdes-Tresanco-MS in #1239
write PDB conect records for S-S bridges and HETATM by @Valdes-Tresanco-MS in #1240
Fix bug for nbfix/chamber in ParmEd v3.4 by @swails in #1282

Full Changelog: 3.4.3...3.4.4

ParmEd v3.4.3

2021-08-31T14:16:21Z

Finish ParmEd fixes for OpenMM 7.6 compatibility

ParmEd v3.4.2

2021-08-28T01:55:58Z

Fix support for OpenMM 7.6