Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / openmm/openmmforcefields issues and pull requests
#295 - Incomplete GROMACS top file when using openff with parmed or interchange for GAFF
Issue -
State: open - Opened by pablo-osmo about 1 year ago
- 1 comment
#294 - Ff string
Pull Request -
State: closed - Opened by mikemhenry about 1 year ago
- 4 comments
#293 - Fix system and template generator for Espaloma 0.3.*
Pull Request -
State: open - Opened by ijpulidos about 1 year ago
#292 - Error on custom force
Pull Request -
State: closed - Opened by mattwthompson about 1 year ago
- 3 comments
#291 - Amber Lipid21 two 1-4 scaling error
Issue -
State: open - Opened by gohdavid about 1 year ago
- 3 comments
#290 - Scattered fixes to get CI running
Pull Request -
State: closed - Opened by mattwthompson about 1 year ago
- 8 comments
#289 - [DNM] Pinning ambertools version to <= 22
Pull Request -
State: closed - Opened by ijpulidos about 1 year ago
- 13 comments
#288 - Allow parsing of offxml strings
Pull Request -
State: closed - Opened by jthorton about 1 year ago
- 9 comments
#287 - Do not use old OpenFF Toolkit versions
Pull Request -
State: closed - Opened by mattwthompson about 1 year ago
- 2 comments
#286 - Pin to ambertools <= 22 until we can sort out changes to GAFF2 behavior
Issue -
State: closed - Opened by jchodera about 1 year ago
- 3 comments
#285 - Allow passing a toolkit registry through to SystemGenerator
Issue -
State: open - Opened by IAlibay about 1 year ago
- 2 comments
#284 - Create UFFTemplateGenerator
Issue -
State: open - Opened by jchodera over 1 year ago
#283 - Failure to locate and parse OpenFF force fields
Issue -
State: closed - Opened by nielskm over 1 year ago
- 10 comments
#282 - Check if partial charges are preserved when using `from-molecule` charge method in `EspalomaTemplateGenerator`
Issue -
State: open - Opened by ijpulidos over 1 year ago
- 2 comments
Labels: bug
#281 - AmberTools 23 causes openmmforcefield tests to fail
Issue -
State: open - Opened by jchodera over 1 year ago
- 2 comments
#280 - Update to AmberTools23
Issue -
State: open - Opened by jchodera over 1 year ago
#279 - Add CI test branches with and without OpenEye license
Issue -
State: open - Opened by jchodera over 1 year ago
- 1 comment
#278 - Fix failing tests
Issue -
State: open - Opened by jchodera over 1 year ago
#277 - Removing Openeye from CI
Pull Request -
State: closed - Opened by ijpulidos over 1 year ago
- 2 comments
#276 - Grab forcefield from URL
Issue -
State: closed - Opened by mikemhenry over 1 year ago
- 2 comments
#275 - Plugin architecture?
Issue -
State: open - Opened by jchodera over 1 year ago
- 2 comments
#274 - Switch to `setup-micromamba`
Pull Request -
State: closed - Opened by mattwthompson over 1 year ago
#273 - Fix OPC3 bond length
Pull Request -
State: closed - Opened by mattwthompson over 1 year ago
- 1 comment
#272 - Incorrect H-O bond length in Amber OPC3
Issue -
State: closed - Opened by chapincavender over 1 year ago
#271 - Fix Espaloma system/template generator
Pull Request -
State: open - Opened by kntkb over 1 year ago
- 3 comments
#270 - Bump codecov/codecov-action from 3.1.1 to 3.1.4
Pull Request -
State: open - Opened by dependabot[bot] over 1 year ago
- 1 comment
Labels: dependencies
#269 - source of amber ion parameters
Issue -
State: open - Opened by thempel over 1 year ago
- 1 comment
#268 - Do not load water models as small molecule force fields
Pull Request -
State: closed - Opened by mattwthompson over 1 year ago
- 2 comments
#267 - Add support for fetching forcefield from URL
Issue -
State: open - Opened by mikemhenry over 1 year ago
- 1 comment
Labels: enhancement, high-priority
#266 - Bump codecov/codecov-action from 3.1.1 to 3.1.3
Pull Request -
State: closed - Opened by dependabot[bot] over 1 year ago
- 1 comment
Labels: dependencies
#265 - Remove OpenEye from CI
Pull Request -
State: closed - Opened by mikemhenry over 1 year ago
- 17 comments
#264 - Add support to load espaloma models trained using dropouts and batch normalization
Pull Request -
State: closed - Opened by kntkb over 1 year ago
- 2 comments
#263 - EspalomaTemplateGenerator cannot properly load espaloma models trained with dropouts and batch normalization
Issue -
State: open - Opened by kntkb over 1 year ago
#262 - Bump codecov/codecov-action from 3.1.1 to 3.1.2
Pull Request -
State: closed - Opened by dependabot[bot] over 1 year ago
- 1 comment
Labels: dependencies
#261 - Best way to protonate ligands / small molecules to get them ready for GAFF
Issue -
State: open - Opened by razvanmarinescu over 1 year ago
- 1 comment
#260 - GAFF - ValueError: No template found for residue 571 (58H) - MWE
Issue -
State: closed - Opened by razvanmarinescu over 1 year ago
- 11 comments
#259 - Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry.
Issue -
State: closed - Opened by razvanmarinescu over 1 year ago
- 4 comments
#258 - Support more platforms
Issue -
State: open - Opened by peastman over 1 year ago
- 7 comments
#257 - Trying to use GAFF. How do I generate a SMILES code so I can create the molecule?
Issue -
State: closed - Opened by razvanmarinescu over 1 year ago
- 9 comments
#256 - No module named 'openff.units'
Issue -
State: closed - Opened by pablo-arantes almost 2 years ago
- 8 comments
#255 - If possible, how to output the generated GAFF parameters in .xml format?
Issue -
State: closed - Opened by taoliu032 almost 2 years ago
- 11 comments
#254 - Loading .off and .frcmod files
Issue -
State: closed - Opened by pguillem almost 2 years ago
#253 - SystemGenerator should only add barostat if system is periodic
Pull Request -
State: closed - Opened by jchodera almost 2 years ago
- 5 comments
#252 - MonteCarloBarostat is added to non-periodic systems if `barostat` is specified to SystemGenerator
Issue -
State: closed - Opened by jchodera almost 2 years ago
Labels: bug
#251 - How can I convert charmm interface FF to openmm xml?
Issue -
State: open - Opened by wangm23456 almost 2 years ago
- 1 comment
#250 - Set 1-4 scaling factors from values specified in force field
Pull Request -
State: closed - Opened by mattwthompson almost 2 years ago
#249 - OpenEye license expired
Issue -
State: closed - Opened by mattwthompson almost 2 years ago
- 1 comment
#248 - Error if custom force is found
Pull Request -
State: closed - Opened by mattwthompson almost 2 years ago
- 4 comments
#247 - Support custom openmm forces
Issue -
State: open - Opened by jthorton almost 2 years ago
- 6 comments
#246 - add options to deploy espaloma system
Pull Request -
State: closed - Opened by kntkb almost 2 years ago
- 2 comments
#245 - [Enhancement] Add options to EspalomaTemplateGenerator to deploy different espaloma models
Issue -
State: open - Opened by kntkb almost 2 years ago
#244 - Install newest toolkit
Pull Request -
State: closed - Opened by mattwthompson almost 2 years ago
- 1 comment
#243 - [DNM] Test against OpenMM 8 beta
Pull Request -
State: closed - Opened by mattwthompson almost 2 years ago
- 1 comment
#242 - Convert all amber ions
Pull Request -
State: closed - Opened by mattwthompson almost 2 years ago
- 9 comments
#241 - << OpenMM forcefield for organic/inorganic systems >>
Issue -
State: open - Opened by icamps almost 2 years ago
- 4 comments
#240 - Update docstrings, run in CI
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 2 comments
#239 - Convert all amber ions; add OPC and OPC3 waters
Pull Request -
State: closed - Opened by aizvorski about 2 years ago
- 10 comments
#238 - Bump codecov/codecov-action from 3.1.0 to 3.1.1
Pull Request -
State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies
#237 - make sure we don't install the newest toolkit by mistake
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 15 comments
#236 - [DNM] #227 with codecov action
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 2 comments
#235 - Directly run and upload coverage report
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
#234 - Turn off macos + Python 3.10 tests
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 3 comments
#233 - AttributeError: 'Atom' object has no attribute 'element'
Issue -
State: closed - Opened by arjunNUFC about 2 years ago
- 9 comments
#232 - Tweak CI: Switch to Micromamba, pin to supported OpenFF Toolkit versions
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 5 comments
#231 - Do not symlink files in installation
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 1 comment
#230 - Fix/remove sym links
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 3 comments
#229 - Do not symlink data files in `setup.py`
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 1 comment
#228 - Trouble creating RNA system with espaloma
Issue -
State: closed - Opened by kntkb about 2 years ago
- 3 comments
#227 - Fix toolkit tests
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 24 comments
#226 - add back in openeye toolkit
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 1 comment
#225 - Fix OpenFF toolkit tests and compatibility
Pull Request -
State: closed - Opened by mattwthompson about 2 years ago
- 14 comments
#224 - Use parameterized small molecules in a complex
Issue -
State: closed - Opened by zlcrrrr about 2 years ago
- 1 comment
#223 - fix syntax issues
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
- 1 comment
#222 - No template found for residue 1 (MOH)
Issue -
State: closed - Opened by ziyuanzhao2000 about 2 years ago
- 3 comments
#221 - Add test branch for latest preview of OpenFF toolkit
Issue -
State: closed - Opened by jchodera about 2 years ago
- 1 comment
#220 - remove oe license check
Pull Request -
State: closed - Opened by mikemhenry about 2 years ago
#219 - Fix #215: Copy gaff dat file to temp dir
Pull Request -
State: closed - Opened by rosemary-cresset about 2 years ago
- 2 comments
#218 - Fix #214: Leave temp dir before raising exceptions
Pull Request -
State: closed - Opened by rosemary-cresset about 2 years ago
#217 - Fix #216: Remove % sign from parmchk2 command
Pull Request -
State: closed - Opened by rosemary-cresset about 2 years ago
#216 - Errant percentage sign in string stops parmchk2 from running successfully on some Windows machines
Issue -
State: closed - Opened by rosemary-cresset about 2 years ago
#215 - parmchk2 fails to run if openmmforcefields is installed somewhere with spaces in the path
Issue -
State: closed - Opened by rosemary-cresset about 2 years ago
- 2 comments
#214 - Recursive exception makes it very difficult to read acdoctor error message on Windows
Issue -
State: closed - Opened by rosemary-cresset about 2 years ago
#213 - Fix #211 : Use basename instead of full path for cache database table names
Pull Request -
State: closed - Opened by jchodera about 2 years ago
- 1 comment
#212 - Fix #210: gaff atom type name is now correctly passed
Pull Request -
State: closed - Opened by jchodera about 2 years ago
Labels: bug
#211 - SMIRNOFFTemplateGenerator cache database table name should be file name not file path
Issue -
State: closed - Opened by rosemary-cresset about 2 years ago
Labels: bug
#210 - Atom typing always uses GAFF even when GAFF2 specified
Issue -
State: closed - Opened by rosemary-cresset about 2 years ago
- 2 comments
Labels: bug, high-priority
#209 - Using CHARMM36 leads to `ValueError: Found multiple NonbondedForce tags with different 1-4 scales`
Issue -
State: closed - Opened by ljmartin about 2 years ago
- 2 comments
Labels: wontfix
#208 - Fix accidental elimination of torsions after 0.11.0 release
Pull Request -
State: closed - Opened by jchodera about 2 years ago
- 15 comments
Labels: bug, high-priority
#207 - Add `allow_nonintegral_charges` optional argument to enable user-provided nonintegral charges
Issue -
State: open - Opened by jchodera about 2 years ago
Labels: bug
#206 - carboxylate modeling problem
Issue -
State: closed - Opened by OkKakao over 2 years ago
- 1 comment
#205 - No module named Openforcefield
Issue -
State: closed - Opened by manos996 over 2 years ago
- 4 comments
#204 - Exception: Relative force deviation for [H]C(=O)[H]
Issue -
State: closed - Opened by mikemhenry over 2 years ago
- 1 comment
Labels: bug, high-priority
#203 - Some parameters missing from phosaa14SB.xml
Issue -
State: open - Opened by rosemary-cresset over 2 years ago
Labels: bug
#202 - Fix CI
Pull Request -
State: closed - Opened by mikemhenry over 2 years ago
- 1 comment
#201 - Remove espaloma debug line
Pull Request -
State: closed - Opened by mikemhenry over 2 years ago
#200 - Noisy debug prints at INFO logging level
Issue -
State: closed - Opened by IAlibay over 2 years ago
- 1 comment
#199 - Removed leftover debug line
Pull Request -
State: closed - Opened by richardjgowers over 2 years ago
- 1 comment
#198 - Remove debug prints.
Pull Request -
State: closed - Opened by ijpulidos over 2 years ago
#197 - Bump codecov/codecov-action from 2.1.0 to 3.1.0
Pull Request -
State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies
#196 - Bump actions/checkout from 2 to 3.0.2
Pull Request -
State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies