Ecosyste.ms: Issues

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GitHub / choderalab/yank issues and pull requests

#1304 - Silent GAFF2 failures can happen easily

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

#1301 - support for python 3.10?

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

#1300 - problem during absolute binding energy calculation

Issue - State: open - Opened by mayank-kohli over 1 year ago - 3 comments

#1299 - Failures due to API changes in `openmmtools`

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

#1296 - multichain receptor for 'restrained_receptor_atoms'

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

#1295 - I got the following error.

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

#1294 - pymbar 4 compatibility

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

#1293 - Load() missing one argument

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

#1292 - Free energy of solvation for charged ligand

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

#1290 - Update CI

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

#1289 - a error about antecamber

Issue - State: open - Opened by kingljy0818 about 2 years ago - 5 comments

#1288 - Yank installation Python3.10 import error

Issue - State: open - Opened by JonaTheHutt about 2 years ago - 1 comment

#1287 - Migrate thermodynamic trailblazing to openmmtools

Issue - State: open - Opened by jchodera about 2 years ago
Labels: refactoring

#1286 - Fix/support python 310

Pull Request - State: open - Opened by mikemhenry about 2 years ago - 4 comments

#1285 - pin pymbar to stay on 3.x version

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

#1284 - Add Python 3.9 and 3.10 to CI matrix

Pull Request - State: closed - Opened by mattwthompson about 2 years ago - 4 comments

#1283 - extend on resume

Pull Request - State: open - Opened by jfennick about 2 years ago - 1 comment

#1282 - generate_free_energy() fails because standard state correction is missing from the reporter

Issue - State: open - Opened by zhang-ivy about 2 years ago - 1 comment
Labels: bug, Priority high

#1281 - Cannot apply the restraint. No receptor-ligand complex could be found.

Issue - State: open - Opened by j-kedzierski about 2 years ago - 1 comment

#1279 - Yank analysis error

Issue - State: closed - Opened by kingljy0818 over 2 years ago - 7 comments

#1277 - Is it possible to use enhanced sampling algorithms such as REST/REST2?

Issue - State: open - Opened by jackzzs over 2 years ago - 1 comment

#1273 - Windows CI is failing

Issue - State: closed - Opened by mjw99 over 2 years ago - 1 comment

#1272 - Updated docker image for YANK

Issue - State: open - Opened by mmagithub over 2 years ago - 11 comments

#1271 - Add CITATION.cff file

Issue - State: open - Opened by mikemhenry over 2 years ago

#1270 - Update continuous integration

Issue - State: open - Opened by jchodera over 2 years ago
Labels: testing

#1269 - Check attributes accessed in ExperimentAnalyzer.__del__

Issue - State: open - Opened by lilyminium over 2 years ago

#1268 - Update yaml loader in analyze.py

Pull Request - State: open - Opened by lilyminium over 2 years ago - 1 comment

#1267 - Stable minimization

Pull Request - State: open - Opened by jfennick over 2 years ago - 2 comments

#1266 - Protocol to mutate a chemical?

Issue - State: open - Opened by chabi-fin over 2 years ago

#1265 - YANK analyze error

Issue - State: open - Opened by MehreenZaka over 2 years ago - 2 comments

#1264 - yank-example-hydration-phenol-Analysis-error

Issue - State: open - Opened by owenustc over 2 years ago - 1 comment

#1263 - Update for new OpenMM Namespace

Pull Request - State: open - Opened by mikemhenry almost 3 years ago - 5 comments

#1262 - how to get openMM yank free energy per time

Issue - State: open - Opened by Byun-jinyoung almost 3 years ago

#1261 - Platform-specific energy differences with OpenMM 7.5.1 vs 7.6

Issue - State: closed - Opened by mattwthompson almost 3 years ago - 9 comments

#1260 - Module not found after yank update

Issue - State: open - Opened by gsabbih6 almost 3 years ago - 6 comments

#1258 - Removed travis CI config file

Pull Request - State: closed - Opened by mikemhenry about 3 years ago

#1256 - NetCDF: HDF error

Issue - State: open - Opened by jslim-furame about 3 years ago - 2 comments

#1255 - ligand position after trailblazing

Issue - State: open - Opened by isjoung about 3 years ago

#1254 - Can yank be used to calculate the binding energy of proteins and peptides?

Issue - State: open - Opened by dxli75 over 3 years ago - 2 comments

#1253 - yank found unknown parameter number_of_iterations in all examples. I changed nothing, just running

Issue - State: open - Opened by dxli75 over 3 years ago - 2 comments
Labels: bug, documentation, examples

#1252 - CRITICAL: Experiment NaN

Issue - State: open - Opened by sadafrani6 over 3 years ago - 2 comments

#1249 - REMD Performance

Issue - State: open - Opened by shitanshu-cell almost 4 years ago - 4 comments

#1248 - Error with reading yaml file

Issue - State: open - Opened by Byun-jinyoung almost 4 years ago - 3 comments

#1247 - Parallel simulation using slurm queue

Issue - State: open - Opened by jslim-furame almost 4 years ago - 3 comments

#1246 - Using yank for calculation of mixing free energy

Issue - State: open - Opened by Eli-VDB almost 4 years ago - 3 comments

#1245 - Tests are failing

Issue - State: open - Opened by jaimergp almost 4 years ago

#1244 - Add GHA CI

Pull Request - State: closed - Opened by jaimergp almost 4 years ago - 1 comment

#1242 - hydration free energy of a molecule with Yank

Issue - State: open - Opened by avdisalem about 4 years ago - 3 comments

#1240 - How to use yank for peptide-protein binding?

Issue - State: open - Opened by aizvorski about 4 years ago - 1 comment

#1239 - GPU compute mode

Issue - State: open - Opened by abazabaaa about 4 years ago

#1238 - NAN issue in hydration free energy calculation

Issue - State: open - Opened by kexul about 4 years ago

#1237 - Question about YANK restrains

Issue - State: open - Opened by mmagithub about 4 years ago

#1236 - Hydration free energy protocol does not turn off steric interaction in vacuum

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

#1235 - CUDA problem

Issue - State: closed - Opened by mmagithub about 4 years ago - 5 comments

#1234 - yank analyze error in restraint energy calculation

Issue - State: closed - Opened by isjoung over 4 years ago - 5 comments

#1233 - IndexError: invalid index to scalar variable.

Issue - State: closed - Opened by aysegulcayir over 4 years ago - 4 comments

#1232 - Fix miniconda install in travis tests

Pull Request - State: closed - Opened by jchodera over 4 years ago - 1 comment

#1231 - Errors with analyse report

Issue - State: open - Opened by kadiliissaar over 4 years ago

#1228 - CRITICAL: Experiment NaN !

Issue - State: open - Opened by kingljy0818 over 4 years ago - 5 comments

#1227 - Incorporate QM into ligand parameterization pipeline

Issue - State: open - Opened by tantrev over 4 years ago - 7 comments

#1226 - Binding pose prediction

Issue - State: open - Opened by daveminh over 4 years ago

#1223 - How to configure yank script when the receptor includes coenzyme

Issue - State: open - Opened by kingljy0818 over 4 years ago - 4 comments

#1222 - How to enable the parallel mode in two gpus server

Issue - State: open - Opened by kingljy0818 over 4 years ago - 4 comments

#1221 - Simulations of molecular melt

Issue - State: closed - Opened by kadiliissaar over 4 years ago - 3 comments

#1220 - Possible issue with net_charge assignment from yaml with antechamber

Issue - State: closed - Opened by mjw99 over 4 years ago - 4 comments

#1219 - [WIP] add support for relative binding free energies

Pull Request - State: open - Opened by ajsilveira over 4 years ago

#1218 - NaN encountered with hydration example in document.

Issue - State: closed - Opened by kexul over 4 years ago - 2 comments

#1217 - Solubility

Issue - State: closed - Opened by kadiliissaar over 4 years ago - 1 comment

#1216 - pinning pymbar version

Pull Request - State: closed - Opened by hannahbrucemacdonald over 4 years ago - 1 comment

#1214 - Trailblazing analysis error

Issue - State: closed - Opened by mjw99 over 4 years ago - 12 comments

#1211 - Use Open Force Field parameters for ligands

Issue - State: open - Opened by daveminh over 4 years ago - 20 comments

#1207 - Added support for CHARMM-format input files (psf/pdb and a list of pr…

Pull Request - State: closed - Opened by jeffcomer over 4 years ago - 7 comments

#1205 - pymbar error!

Issue - State: closed - Opened by sawstory over 4 years ago - 2 comments

#1182 - Binding site identification?

Issue - State: open - Opened by jadeshi about 5 years ago - 2 comments

#1152 - yaml.load issues

Issue - State: open - Opened by jchodera over 5 years ago - 6 comments

#1130 - MPI bug when multiple GPUs are used per calculation

Issue - State: closed - Opened by HershGupta404 over 5 years ago - 8 comments
Labels: bug, repex, critical

#1083 - Failure to set up a single molecule terminates entire MPI calculation

Issue - State: open - Opened by jchodera about 6 years ago - 1 comment
Labels: enhancement, error handling

#760 - Add CHARMM input scheme

Issue - State: closed - Opened by leelasd about 7 years ago - 12 comments
Labels: enhancement

#547 - Add osx travis branch

Pull Request - State: closed - Opened by jchodera almost 8 years ago - 10 comments

#502 - Performance tuning parameters like number of iterations and replicas

Issue - State: closed - Opened by jlerche about 8 years ago - 5 comments