Ecosyste.ms: Issues

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GitHub / ParmEd/ParmEd issues and pull requests

#1354 - problem with combining structures

Issue - State: open - Opened by JuroDobias 15 days ago

#1351 - Ignore TURN comments in PDBs

Pull Request - State: open - Opened by slochower about 1 month ago - 1 comment

#1350 - fix `SyntaxWarning: invalid escape sequence`

Pull Request - State: open - Opened by njzjz about 1 month ago

#1349 - darwin_major_to_osx_map needs update

Issue - State: open - Opened by eemartin42 about 2 months ago - 4 comments

#1348 - Fix wildcard sorting when writing Amber parameter sets (fixes #1347)

Pull Request - State: closed - Opened by murfalo 2 months ago - 1 comment

#1346 - Add support for 12-6-4 models.

Pull Request - State: closed - Opened by swails 3 months ago - 1 comment

#1345 - Read Gromacs topology file with wrong openmm topology object

Issue - State: open - Opened by yjianzhu 3 months ago - 1 comment

#1344 - Add the support for four new water models to the add12_6_4 in ParmEd

Pull Request - State: closed - Opened by pengfeili1 3 months ago - 1 comment

#1343 - Warning issues about converting gromacs top to Amber

Issue - State: closed - Opened by aw10279 3 months ago - 5 comments

#1342 - OpenMM to Gromacs conversion using ParmEd

Issue - State: closed - Opened by sameersaurav 3 months ago - 2 comments

#1341 - Example Convert the gromacs topology file to the charmm topology file

Issue - State: open - Opened by herbrexe 4 months ago - 2 comments

#1341 - Example Convert the gromacs topology file to the charmm topology file

Issue - State: open - Opened by herbrexe 4 months ago - 2 comments

#1340 - AttributeError: module 'parmed' has no attribute 'load_file'

Issue - State: closed - Opened by skipper2cic 4 months ago - 1 comment

#1339 - LJ repulsion

Issue - State: closed - Opened by JaimeRubioMartinez 4 months ago - 2 comments

#1338 - parmed.strip() fails to strip correct mask

Issue - State: closed - Opened by pguillem 5 months ago - 1 comment

#1335 - tests failed on riscv64 and mips64el

Issue - State: open - Opened by yuzibo 6 months ago

#1333 - << Old bug alive? >>

Issue - State: open - Opened by icamps 6 months ago

#1332 - set_version

Issue - State: open - Opened by Alexander-McMahon 7 months ago

#1330 - Fixed Improper Method Call: Replaced `NotImplementedError`

Pull Request - State: open - Opened by fazledyn-or 8 months ago

#1328 - Fixed Improper Method Call: Replaced `mktemp`

Pull Request - State: closed - Opened by fazledyn-or 8 months ago

#1327 - Fix setup.py

Pull Request - State: closed - Opened by swails 8 months ago

#1326 - Fix usage of lru_cache for cache in py38

Pull Request - State: closed - Opened by swails 8 months ago

#1325 - Support Python 3.12

Pull Request - State: closed - Opened by mattwthompson 8 months ago - 7 comments

#1323 - Gromacs pair funct !=1 unknown

Issue - State: open - Opened by JuuelHerza 9 months ago - 2 comments

#1322 - load_file method does not populate angles

Issue - State: closed - Opened by mmfarrugia 9 months ago - 4 comments

#1321 - GromacsError: Only 3-point vsite type 1 is supported

Issue - State: open - Opened by ale94mleon 9 months ago - 1 comment

#1319 - Fix Python 3.8 support

Pull Request - State: closed - Opened by swails 10 months ago

#1318 - python 3.8 incompatibility from functools.cache issue

Issue - State: closed - Opened by mmfarrugia 10 months ago - 4 comments

#1317 - rename residue PDB to be compatible with PDB

Issue - State: open - Opened by groponp 10 months ago

#1314 - Remove unused scripts

Pull Request - State: closed - Opened by swails 11 months ago - 1 comment

#1313 - Unexpected change of [ constraints ] to [ settles ]

Issue - State: open - Opened by ale94mleon 11 months ago - 1 comment

#1312 - Problem with non-contiguous atoms

Issue - State: open - Opened by aminsagar 11 months ago - 2 comments

#1311 - Basic routines for internal to cartesian coordinate conversion

Pull Request - State: closed - Opened by bradakta about 1 year ago - 1 comment

#1310 - Transfer chain IDs to OpenMM topology.

Pull Request - State: closed - Opened by jpthompson17 about 1 year ago - 1 comment

#1309 - warnings for ANISOU records?

Issue - State: open - Opened by bradakta about 1 year ago - 1 comment

#1308 - how to add non-natural amino acid?

Issue - State: open - Opened by Yiwenxx7 about 1 year ago - 1 comment

#1307 - energy_decomposition from openmm run

Issue - State: closed - Opened by spadavec about 1 year ago - 4 comments

#1306 - Flip guess strategy for atomic numbers

Pull Request - State: closed - Opened by bradakta about 1 year ago - 6 comments

#1305 - Added 3D-RISM and GBNSR6 to mdin configuration

Pull Request - State: closed - Opened by Valdes-Tresanco-MS about 1 year ago

#1304 - Preserve formal charges from PDB and CIF files if present over templates

Pull Request - State: closed - Opened by swails about 1 year ago

#1303 - Fix bug with restart reporter for OpenMM minimization

Pull Request - State: closed - Opened by nffaruk about 1 year ago - 1 comment

#1302 - Fix bug with adding positional restraints for OpenMM (ParmEd#1301)

Pull Request - State: closed - Opened by nffaruk about 1 year ago - 1 comment

#1301 - Error when using restraints with OpenMM within ParmEd

Issue - State: closed - Opened by nabilfarukqtx about 1 year ago - 1 comment

#1299 - Fix an error with mdin changing

Pull Request - State: closed - Opened by swails over 1 year ago

#1298 - Gromacs to AMBER issue with torsion

Issue - State: open - Opened by mmagithub over 1 year ago - 9 comments

#1297 - Why are include statements not written to output top?

Issue - State: open - Opened by noahharrison64 over 1 year ago - 2 comments

#1296 - Single Point Energy Calculation with OpenMM and CHARMM

Issue - State: open - Opened by Sulstice over 1 year ago

#1294 - annotating atom types in a gromacs processed topology

Issue - State: open - Opened by Dan-Burns over 1 year ago - 4 comments

#1291 - ImportError when creating system with rst7 and parm7 files

Issue - State: closed - Opened by slweng0321 over 1 year ago - 3 comments

#1290 - switch out copy with deepcopy for structure.copy() method

Pull Request - State: closed - Opened by daico007 over 1 year ago

#1288 - Box dimensions not read from NetCDF Restart?

Issue - State: closed - Opened by bradakta over 1 year ago - 1 comment

#1287 - Convert .xml format to gromacs format

Issue - State: open - Opened by howlfwq over 1 year ago - 1 comment

#1286 - Improve rdkit coordinate precision

Pull Request - State: open - Opened by bradakta over 1 year ago - 2 comments

#1285 - set `python_requires` to `>=3.8`

Pull Request - State: closed - Opened by njzjz over 1 year ago - 1 comment

#1284 - Improve CIF and PDB parsing and add informatics fields to Atom and Bond

Pull Request - State: closed - Opened by swails over 1 year ago

#1283 - Can I convert .dat or .prep file from glycam?

Issue - State: open - Opened by OkKakao over 1 year ago - 1 comment

#1282 - Fix bug for nbfix/chamber in ParmEd v3.4

Pull Request - State: closed - Opened by swails over 1 year ago

#1281 - Fix bug reported by Alex Sodt

Pull Request - State: closed - Opened by swails over 1 year ago

#1280 - problem with nbfix and charmm

Issue - State: closed - Opened by dacase over 1 year ago - 1 comment

#1278 - Prefer patch versions that replace external bonds

Pull Request - State: closed - Opened by peastman over 1 year ago - 4 comments

#1277 - Enable changing C4 terms in LJ pairs individually

Pull Request - State: closed - Opened by KevinMei-Github over 1 year ago - 1 comment

#1276 - Matching patches to residues

Issue - State: open - Opened by peastman over 1 year ago - 19 comments

#1275 - Set atomic number when applying a patch

Pull Request - State: closed - Opened by peastman over 1 year ago - 5 comments

#1274 - Drude psf where NUMANISO is zero

Pull Request - State: closed - Opened by florianjoerg over 1 year ago - 1 comment

#1272 - Fails to construct a system from own-written PSF file

Issue - State: open - Opened by merkys over 1 year ago - 1 comment

#1271 - Multiple mutations in multiple chains in timerge

Issue - State: open - Opened by Qianchen-Liu over 1 year ago

#1270 - How can I convert Gromacs top file into CHARMM file?

Issue - State: open - Opened by OkKakao almost 2 years ago

#1269 - Delete test_parmed_visualization.py

Pull Request - State: closed - Opened by swails almost 2 years ago

#1268 - Would you release the next version of Parmed.

Issue - State: open - Opened by felix5572 almost 2 years ago

#1267 - More compound generate.

Issue - State: open - Opened by Aunity almost 2 years ago - 1 comment
Labels: bug

#1266 - lonepair refinement

Pull Request - State: closed - Opened by JohannesKarwou almost 2 years ago

#1265 - TiMerge Not working

Issue - State: open - Opened by Mag14011 almost 2 years ago

#1264 - ff19SB CMAP not supported when using tiMerge command.

Issue - State: closed - Opened by josiahbones almost 2 years ago - 3 comments

#1263 - Ignore blank lines in mol2

Pull Request - State: closed - Opened by adw62 almost 2 years ago

#1262 - Gromacs to Amber conversion -- ion clustering

Issue - State: open - Opened by TienMPhan almost 2 years ago

#1261 - Patching tyrosine to phosphotyrosine failed with CHARMM36 files

Issue - State: open - Opened by zzhangzzhang almost 2 years ago - 1 comment

#1260 - Problem with `__getitem__()` when using inheritance and required arguments

Issue - State: open - Opened by bradakstx almost 2 years ago - 1 comment

#1259 - Add a volume property

Pull Request - State: open - Opened by bradakstx almost 2 years ago - 3 comments

#1258 - openmm.load_topology DrudeAtom support

Issue - State: open - Opened by florianjoerg almost 2 years ago - 1 comment

#1257 - openmm.load_topology() missing RB improper dihedrals

Issue - State: open - Opened by HUANGZR86 almost 2 years ago - 2 comments