Ecosyste.ms: Issues

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GitHub / ParmEd/ParmEd issues and pull requests

#1385 - Copy impropers when compressing

Pull Request - State: open - Opened by epretti 5 days ago

#1381 - Using Parmed to writeout parm7 and rst7 files for OpenMM system

Issue - State: open - Opened by dim-99 2 months ago - 1 comment

#1380 - Plans for a new release?

Issue - State: closed - Opened by chrisjonesBSU 3 months ago - 4 comments

#1379 - Using ParmEd with openMM

Issue - State: open - Opened by tejtaruns 4 months ago - 1 comment

#1378 - Switch to non-deprecated miniforge

Pull Request - State: closed - Opened by swails 4 months ago

#1377 - Fixed deepcopy for Atom.

Pull Request - State: open - Opened by ywu 4 months ago - 4 comments

#1375 - Bond order lost after serializing Structure

Issue - State: closed - Opened by SHZ66 5 months ago - 2 comments

#1374 - Fixed compatibility with NumPy 2.0+

Pull Request - State: closed - Opened by vedranmiletic 5 months ago - 4 comments

#1372 - Gromacs topology to Amber Topology

Issue - State: open - Opened by Kapalisuri 5 months ago

#1371 - Conversion of GROMACS TRAJECTORY TO AMBER TRAJECTORY

Issue - State: open - Opened by Kapalisuri 5 months ago - 1 comment

#1370 - Fix the build wrt RDKit package issues

Pull Request - State: closed - Opened by swails 5 months ago

#1368 - Ensure PBC box vectors are in reduced form for OpenMM

Pull Request - State: closed - Opened by nffaruk 5 months ago

#1367 - Fix velocity unit scale for existing vels passed to OpenMM

Pull Request - State: closed - Opened by nffaruk 5 months ago - 1 comment

#1364 - Incompatible with NumPy 2.0

Issue - State: closed - Opened by njzjz 6 months ago

#1363 - PDB -> parm7 and rst7

Issue - State: open - Opened by johnnytam100 6 months ago - 1 comment

#1362 - [Gromber] non-contiguous molecules

Issue - State: open - Opened by slweng0321 7 months ago - 7 comments

#1361 - AttributeError: 'AmberParameterSet' object has no attribute 'save'

Issue - State: open - Opened by qlearn-code 7 months ago - 2 comments

#1360 - Bugfixed AtomType equality operator

Pull Request - State: closed - Opened by murfalo 7 months ago - 1 comment

#1358 - Remove amber improper sorting

Pull Request - State: open - Opened by murfalo 7 months ago

#1356 - Fix a bug reported via email

Pull Request - State: open - Opened by swails 7 months ago

#1355 - Fix output of changeLJSingleType

Pull Request - State: closed - Opened by swails 7 months ago

#1354 - problem with combining structures

Issue - State: open - Opened by JuroDobias 8 months ago - 2 comments

#1351 - Ignore TURN comments in PDBs

Pull Request - State: closed - Opened by slochower 8 months ago - 1 comment

#1350 - fix `SyntaxWarning: invalid escape sequence`

Pull Request - State: closed - Opened by njzjz 9 months ago

#1349 - darwin_major_to_osx_map needs update

Issue - State: open - Opened by eemartin42 9 months ago - 4 comments

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

Pull Request - State: closed - Opened by murfalo 9 months ago - 1 comment

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

Pull Request - State: closed - Opened by swails 10 months ago - 1 comment

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

Issue - State: open - Opened by yjianzhu 10 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 10 months ago - 1 comment

#1343 - Warning issues about converting gromacs top to Amber

Issue - State: closed - Opened by aw10279 10 months ago - 5 comments

#1342 - OpenMM to Gromacs conversion using ParmEd

Issue - State: closed - Opened by sameersaurav 11 months ago - 2 comments

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

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

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

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

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

Issue - State: closed - Opened by skipper2cic 11 months ago - 1 comment

#1339 - LJ repulsion

Issue - State: closed - Opened by JaimeRubioMartinez 11 months ago - 2 comments

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

Issue - State: closed - Opened by pguillem 12 months ago - 1 comment

#1335 - tests failed on riscv64 and mips64el

Issue - State: open - Opened by yuzibo about 1 year ago

#1334 - Issue with saving modified dihedral parameters into prmtop file

Issue - State: open - Opened by Madu86 about 1 year ago - 1 comment

#1333 - << Old bug alive? >>

Issue - State: open - Opened by icamps about 1 year ago

#1332 - set_version

Issue - State: open - Opened by Alexander-McMahon about 1 year ago

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

Pull Request - State: open - Opened by fazledyn-or about 1 year ago

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

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

#1327 - Fix setup.py

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

#1326 - Fix usage of lru_cache for cache in py38

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

#1325 - Support Python 3.12

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 7 comments

#1323 - Gromacs pair funct !=1 unknown

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

#1322 - load_file method does not populate angles

Issue - State: closed - Opened by mmfarrugia over 1 year ago - 4 comments

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

Issue - State: open - Opened by ale94mleon over 1 year ago - 1 comment

#1319 - Fix Python 3.8 support

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

#1318 - python 3.8 incompatibility from functools.cache issue

Issue - State: closed - Opened by mmfarrugia over 1 year ago - 4 comments

#1317 - rename residue PDB to be compatible with PDB

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

#1314 - Remove unused scripts

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

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

Issue - State: open - Opened by ale94mleon over 1 year ago - 1 comment

#1312 - Problem with non-contiguous atoms

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

#1311 - Basic routines for internal to cartesian coordinate conversion

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

#1310 - Transfer chain IDs to OpenMM topology.

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

#1309 - warnings for ANISOU records?

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

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

Issue - State: open - Opened by Yiwenxx7 almost 2 years ago - 1 comment

#1307 - energy_decomposition from openmm run

Issue - State: closed - Opened by spadavec almost 2 years ago - 4 comments

#1306 - Flip guess strategy for atomic numbers

Pull Request - State: closed - Opened by bradakta almost 2 years ago - 6 comments

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

Pull Request - State: closed - Opened by Valdes-Tresanco-MS almost 2 years ago

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

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

#1303 - Fix bug with restart reporter for OpenMM minimization

Pull Request - State: closed - Opened by nffaruk almost 2 years ago - 1 comment

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

Pull Request - State: closed - Opened by nffaruk almost 2 years ago - 1 comment

#1301 - Error when using restraints with OpenMM within ParmEd

Issue - State: closed - Opened by nabilfarukqtx almost 2 years ago - 1 comment

#1299 - Fix an error with mdin changing

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

#1298 - Gromacs to AMBER issue with torsion

Issue - State: open - Opened by mmagithub almost 2 years ago - 9 comments

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

Issue - State: open - Opened by noahharrison64 almost 2 years ago - 2 comments

#1296 - Single Point Energy Calculation with OpenMM and CHARMM

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

#1294 - annotating atom types in a gromacs processed topology

Issue - State: open - Opened by Dan-Burns almost 2 years ago - 4 comments

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

Issue - State: closed - Opened by slweng0321 almost 2 years ago - 3 comments

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

Pull Request - State: closed - Opened by daico007 almost 2 years ago

#1289 - Some properties are copied by reference in Structure.copy()

Issue - State: closed - Opened by daico007 almost 2 years ago

#1288 - Box dimensions not read from NetCDF Restart?

Issue - State: closed - Opened by bradakta almost 2 years ago - 1 comment