choderalab/yank

Issues

• Problem facing while generating Boresch restraints

  #1313 opened 3 months ago by shilpa888
  0

• YANK Support for Multiple Conformational States

  #1312 opened 7 months ago by mmahmedgithub
  0

• Calculate Free binding energy without schrodingers suite

  #1311 opened 10 months ago by FlorianSchustek3T
  0

• Clarification on why vacuum simulation needed for hydration free energy

  #1310 opened a year ago by zanebeckwith
  2

• leap returned non-zero exit status 31

  #1309 opened a year ago by sobertie
  0

• unallowed value hdac11-ft895

  #1308 opened a year ago by sobertie
  0

• Varying free energy estimates depending on sampler used

  #1307 opened a year ago by thomas-elix
  0

• support Membrane Protein Systems ?

  #1306 opened a year ago by ErikZhang-9762
  0

• Stalling on multiple SLURM nodes

  #1305 opened a year ago by yanze039
  8

• Issue in Yank's calls to OpenMMTools MultiStateReporter

  #1302 opened 2 years ago by sukritsingh
  1

• Silent GAFF2 failures can happen easily

  #1304 opened a year ago by simonaxelrod
  0

• Failures due to API changes in `openmmtools`

  #1299 opened 2 years ago by mattwthompson
  3

• Issue with Ligand Coordinates During Absolute-Binding Free Energy

  #1297 opened 2 years ago by davidcooper7
  0

• Question: How to measure simulation time and how much is necessary?

  #1303 opened 2 years ago by sammun-insitro
  0

• support for python 3.10?

  #1301 opened 2 years ago by zhang-ivy
  2

• problem during absolute binding energy calculation

  #1300 opened 2 years ago by mayank-kohli
  3

• multichain receptor for 'restrained_receptor_atoms'

  #1296 opened 2 years ago by smutao
  0

• NetCDF upstream changes breaking Yank (and can't update OpenMMtools)

  #1298 opened 2 years ago by sukritsingh
  0

• I got the following error.

  #1295 opened 2 years ago by VirtualChemist
  6

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

  #1281 opened 3 years ago by JacekKedzierski
  1

• pymbar 4 compatibility

  #1294 opened 2 years ago by j-wags
  1

• Load() missing one argument

  #1293 opened 2 years ago by RishalAggarwal
  0

• Free energy of solvation for charged ligand

  #1292 opened 2 years ago by moradza
  0

• The periodic box size has decreased to less than twice the nonbonded cutoff

  #1291 opened 2 years ago by vemaparna
  0

• a error about antecamber

  #1289 opened 2 years ago by kingljy0818
  5

• Yank installation Python3.10 import error

  #1288 opened 2 years ago by JonaTheHutt
  1

• Migrate thermodynamic trailblazing to openmmtools

  #1287 opened 2 years ago by jchodera
  0

• NetCDF: HDF error

  #1256 opened 4 years ago by jslim-furame
  2

• Update continuous integration

  #1270 opened 3 years ago by jchodera
  0

• generate_free_energy() fails because standard state correction is missing from the reporter

  #1282 opened 2 years ago by zhang-ivy
  1

• Issues about the calculation of solvation free energy in organic solvent

  #1280 opened 3 years ago by Dropletsimuli
  0

• difference in experimental and calculated binding free energy for p-xylene -T4Lysozyme example

  #1278 opened 3 years ago by vemaparna
  6

• Yank analysis error

  #1279 opened 3 years ago by kingljy0818
  7

• Is it possible to use enhanced sampling algorithms such as REST/REST2?

  #1277 opened 3 years ago by jackzzs
  1

• T4 lysozyme example with implicit solvent runs out of memory when lots of memory appears to be available

  #1276 opened 3 years ago by therealchrisneale
  0

• conda yank install fails while attempting to create symbolic link in root while requesting non-root install

  #1274 opened 3 years ago by therealchrisneale
  1

• t4 lysozyme tutorial with implicit solvent appears to hang at first instance of execute _propagate_replica()

  #1275 opened 3 years ago by therealchrisneale
  0

• Updated docker image for YANK

  #1272 opened 3 years ago by mmagithub
  11

• Windows CI is failing

  #1273 opened 3 years ago by mjw99
  1

• Add CITATION.cff file

  #1271 opened 3 years ago by mikemhenry
  0

• Check attributes accessed in ExperimentAnalyzer.__del__

  #1269 opened 3 years ago by lilyminium
  0

• yank-example-hydration-phenol-Analysis-error

  #1264 opened 3 years ago by owenustc
  1

• Protocol to mutate a chemical?

  #1266 opened 3 years ago by chabi-fin
  0

• Module not found after yank update

  #1260 opened 3 years ago by gsabbih6
  6

• Platform-specific energy differences with OpenMM 7.5.1 vs 7.6

  #1261 opened 3 years ago by mattwthompson
  9

• YANK analyze error

  #1265 opened 3 years ago by MehreenZaka
  2

• how to get openMM yank free energy per time

  #1262 opened 3 years ago by Byun-jinyoung
  0

• Examples and own tests are not working: Stuck at file not found

  #1259 opened 3 years ago by gsabbih6
  0

• ligand position after trailblazing

  #1255 opened 4 years ago by isjoung
  0

• Can yank be used to calculate the binding energy of proteins and peptides?

  #1254 opened 4 years ago by dxli75
  2