Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / ParmEd/ParmEd issues and pull requests
#1354 - problem with combining structures
Issue -
State: open - Opened by JuroDobias 15 days ago
#1353 - Match tleap by ensuring parm{10|99|15}.dat are loaded no more than once
Pull Request -
State: open - Opened by murfalo 22 days ago
#1352 - Loading multiple leaprcs can lead to incorrect parameters due to repeat loading of parm99.dat, parm10.dat, and/or parm15.dat
Issue -
State: open - Opened by murfalo 22 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
#1347 - Amber wildcard impropers are not properly sorted when writing to .frcmod/.parm
Issue -
State: closed - Opened by murfalo 2 months ago
#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
#1344 - Add the support for four new water models to the add12_6_4 in ParmEd
Pull Request -
State: open - Opened by pengfeili1 3 months ago
#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
#1337 - Retrieve bond orders from charmm psf, coordinates and topology + parameter files
Issue -
State: open - Opened by mgoullieux 5 months ago
- 1 comment
#1336 - parmed.openmm.NetCDFReporter format error, cannot open in VMD or MDAnalysis
Issue -
State: open - Opened by ajerschow 6 months ago
#1335 - tests failed on riscv64 and mips64el
Issue -
State: open - Opened by yuzibo 6 months ago
#1334 - Issue with saving modified dihedral parameters into prmtop file
Issue -
State: open - Opened by Madu86 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
#1331 - OPC molecule atoms are not contiguous when saving prmtop file
Issue -
State: open - Opened by emainas 8 months ago
#1330 - Fixed Improper Method Call: Replaced `NotImplementedError`
Pull Request -
State: open - Opened by fazledyn-or 8 months ago
#1329 - add1264.py does not have the C4 parameters fro the OPC water model
Issue -
State: open - Opened by lauricella 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
#1324 - Parmed can not read gromacs topology of water molecules with ifdef statement correctly
Issue -
State: open - Opened by VOD555 8 months ago
#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
#1320 - Is it possible to extract atomtypes, bondtypes, pairtypes, angletypes, dihedraltypes information?
Issue -
State: open - Opened by chaninpark0806 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
#1316 - Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions
Pull Request -
State: closed - Opened by jpthompson17 10 months ago
- 1 comment
#1315 - Add a library of all CCD residues separate from modified amino/nucleic acids
Pull Request -
State: closed - Opened by swails 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
#1300 - Can ParmEd convert a customized amoeba18 force field parameter file to OpenMM xml format?
Issue -
State: closed - Opened by taoliu032 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
#1295 - Splitting prmtop file yields 1 good file and 1 bad file - resulting NTYPES ptr don't match
Issue -
State: closed - Opened by pguillem over 1 year ago
- 5 comments
#1294 - annotating atom types in a gromacs processed topology
Issue -
State: open - Opened by Dan-Burns over 1 year ago
- 4 comments
#1293 - parmed/gromacs/gromacstop.py:525: GromacsWarning: pairs funct != 1; unknown functional parmed/gromacs/gromacstop.py:525:: Too many arguments.
Issue -
State: open - Opened by Eduardneu over 1 year ago
#1292 - CMAPTYPES are differnt when converting Amber topology generated by tleap with ff19SB to a GROMACS topology using ParmEd compared to CHARMM-GUI
Issue -
State: open - Opened by Eduardneu over 1 year ago
- 8 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
#1289 - Some properties are copied by reference in Structure.copy()
Issue -
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
#1279 - combining two structures after saving and reading with pickle does not seem to work
Issue -
State: open - Opened by metma99 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
#1273 - Structure.join_dihedrals() causing problem on copying Structure object.
Issue -
State: open - Opened by WangXinyan940 over 1 year ago
#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