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

#294 - Ff string

Pull Request - State: closed - Opened by mikemhenry 11 months ago - 4 comments

#293 - Fix system and template generator for Espaloma 0.3.*

Pull Request - State: open - Opened by ijpulidos 12 months ago

#292 - Error on custom force

Pull Request - State: closed - Opened by mattwthompson 12 months ago - 3 comments

#291 - Amber Lipid21 two 1-4 scaling error

Issue - State: open - Opened by gohdavid 12 months ago - 3 comments

#290 - Scattered fixes to get CI running

Pull Request - State: closed - Opened by mattwthompson 12 months ago - 8 comments

#289 - [DNM] Pinning ambertools version to <= 22

Pull Request - State: closed - Opened by ijpulidos 12 months ago - 13 comments

#288 - Allow parsing of offxml strings

Pull Request - State: closed - Opened by jthorton 12 months ago - 9 comments

#287 - Do not use old OpenFF Toolkit versions

Pull Request - State: closed - Opened by mattwthompson 12 months ago - 2 comments

#286 - Pin to ambertools <= 22 until we can sort out changes to GAFF2 behavior

Issue - State: closed - Opened by jchodera 12 months ago - 3 comments

#285 - Allow passing a toolkit registry through to SystemGenerator

Issue - State: open - Opened by IAlibay 12 months ago - 2 comments

#284 - Create UFFTemplateGenerator

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

#283 - Failure to locate and parse OpenFF force fields

Issue - State: closed - Opened by nielskm about 1 year ago - 10 comments

#281 - AmberTools 23 causes openmmforcefield tests to fail

Issue - State: open - Opened by jchodera about 1 year ago - 2 comments

#280 - Update to AmberTools23

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

#279 - Add CI test branches with and without OpenEye license

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

#278 - Fix failing tests

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

#277 - Removing Openeye from CI

Pull Request - State: closed - Opened by ijpulidos about 1 year ago - 2 comments

#276 - Grab forcefield from URL

Issue - State: closed - Opened by mikemhenry about 1 year ago - 2 comments

#275 - Plugin architecture?

Issue - State: open - Opened by jchodera about 1 year ago - 2 comments

#274 - Switch to `setup-micromamba`

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

#273 - Fix OPC3 bond length

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

#272 - Incorrect H-O bond length in Amber OPC3

Issue - State: closed - Opened by chapincavender about 1 year ago

#271 - Fix Espaloma system/template generator

Pull Request - State: open - Opened by kntkb about 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] about 1 year ago - 1 comment
Labels: dependencies

#269 - source of amber ion parameters

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

#268 - Do not load water models as small molecule force fields

Pull Request - State: closed - Opened by mattwthompson about 1 year ago - 2 comments

#267 - Add support for fetching forcefield from URL

Issue - State: open - Opened by mikemhenry about 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] about 1 year ago - 1 comment
Labels: dependencies

#265 - Remove OpenEye from CI

Pull Request - State: closed - Opened by mikemhenry about 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 about 1 year ago - 2 comments

#262 - Bump codecov/codecov-action from 3.1.1 to 3.1.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#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

#256 - No module named 'openff.units'

Issue - State: closed - Opened by pablo-arantes over 1 year ago - 8 comments

#255 - If possible, how to output the generated GAFF parameters in .xml format?

Issue - State: closed - Opened by taoliu032 over 1 year ago - 11 comments

#254 - Loading .off and .frcmod files

Issue - State: closed - Opened by pguillem over 1 year ago

#253 - SystemGenerator should only add barostat if system is periodic

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

#251 - How can I convert charmm interface FF to openmm xml?

Issue - State: open - Opened by wangm23456 over 1 year ago - 1 comment

#250 - Set 1-4 scaling factors from values specified in force field

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

#249 - OpenEye license expired

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

#248 - Error if custom force is found

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

#247 - Support custom openmm forces

Issue - State: open - Opened by jthorton over 1 year ago - 6 comments

#246 - add options to deploy espaloma system

Pull Request - State: closed - Opened by kntkb over 1 year ago - 2 comments

#244 - Install newest toolkit

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

#243 - [DNM] Test against OpenMM 8 beta

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

#242 - Convert all amber ions

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 9 comments

#241 - << OpenMM forcefield for organic/inorganic systems >>

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

#240 - Update docstrings, run in CI

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#239 - Convert all amber ions; add OPC and OPC3 waters

Pull Request - State: closed - Opened by aizvorski over 1 year ago - 10 comments

#238 - Bump codecov/codecov-action from 3.1.0 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#237 - make sure we don't install the newest toolkit by mistake

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago - 15 comments

#236 - [DNM] #227 with codecov action

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

#235 - Directly run and upload coverage report

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

#234 - Turn off macos + Python 3.10 tests

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 3 comments

#233 - AttributeError: 'Atom' object has no attribute 'element'

Issue - State: closed - Opened by arjunNUFC almost 2 years ago - 9 comments

#232 - Tweak CI: Switch to Micromamba, pin to supported OpenFF Toolkit versions

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 5 comments

#231 - Do not symlink files in installation

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

#230 - Fix/remove sym links

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago - 3 comments

#229 - Do not symlink data files in `setup.py`

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

#228 - Trouble creating RNA system with espaloma

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

#227 - Fix toolkit tests

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago - 24 comments

#226 - add back in openeye toolkit

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

#225 - Fix OpenFF toolkit tests and compatibility

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 14 comments

#224 - Use parameterized small molecules in a complex

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

#223 - fix syntax issues

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

#222 - No template found for residue 1 (MOH)

Issue - State: closed - Opened by ziyuanzhao2000 almost 2 years ago - 3 comments

#221 - Add test branch for latest preview of OpenFF toolkit

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

#220 - remove oe license check

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

#219 - Fix #215: Copy gaff dat file to temp dir

Pull Request - State: closed - Opened by rosemary-cresset almost 2 years ago - 2 comments

#218 - Fix #214: Leave temp dir before raising exceptions

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

#217 - Fix #216: Remove % sign from parmchk2 command

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

#213 - Fix #211 : Use basename instead of full path for cache database table names

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

#212 - Fix #210: gaff atom type name is now correctly passed

Pull Request - State: closed - Opened by jchodera almost 2 years ago
Labels: bug

#210 - Atom typing always uses GAFF even when GAFF2 specified

Issue - State: closed - Opened by rosemary-cresset almost 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 almost 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 almost 2 years ago - 15 comments
Labels: bug, high-priority

#206 - carboxylate modeling problem

Issue - State: closed - Opened by OkKakao about 2 years ago - 1 comment

#205 - No module named Openforcefield

Issue - State: closed - Opened by manos996 about 2 years ago - 4 comments

#204 - Exception: Relative force deviation for [H]C(=O)[H]

Issue - State: closed - Opened by mikemhenry about 2 years ago - 1 comment
Labels: bug, high-priority

#203 - Some parameters missing from phosaa14SB.xml

Issue - State: open - Opened by rosemary-cresset about 2 years ago
Labels: bug

#202 - Fix CI

Pull Request - State: closed - Opened by mikemhenry about 2 years ago - 1 comment

#201 - Remove espaloma debug line

Pull Request - State: closed - Opened by mikemhenry about 2 years ago

#200 - Noisy debug prints at INFO logging level

Issue - State: closed - Opened by IAlibay about 2 years ago - 1 comment

#199 - Removed leftover debug line

Pull Request - State: closed - Opened by richardjgowers about 2 years ago - 1 comment

#198 - Remove debug prints.

Pull Request - State: closed - Opened by ijpulidos about 2 years ago

#197 - Bump codecov/codecov-action from 2.1.0 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#196 - Bump actions/checkout from 2 to 3.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies