choderalab/espaloma

Issues

• Espaloma Installation

  #222 opened a month ago by chabi-fin
  3

• Systematic approach to parameterise covalently bound ligand

  #219 opened 2 months ago by JSLJ23
  0

• Finetuning Espaloma guide?

  #199 opened a year ago by jarvist
  4

• Assigning Legacy atom types and output topology

  #218 opened 5 months ago by amin-sagar
  0

• Intractable graph size scaling for large proteins

  #217 opened 6 months ago by tristanic
  4

• Test against OpenFF instead of GAFF

  #216 opened 6 months ago by ijpulidos
  0

• SSL: CERTIFICATE_VERIFY_FAILED at "esp.get_model("latest")" step

  #215 opened 8 months ago by beavenah
  6

• Trouble installing "espaloma=0.3.2" from Anaconda

  #213 opened 8 months ago by madilynpaul
  6

• Support for DGL 2.0.x

  #214 opened 8 months ago by ijpulidos
  0

• Parametrization of complex based on PDB and MOL file

  #211 opened 9 months ago by entropybit
  1

• Deployment of espaloma-0.3 for a protein-ligand system

  #212 opened 8 months ago by OleinikovasV
  1

• Atom elements which `espaloma` has been trained on?

  #206 opened 9 months ago by JSLJ23
  2

• Espaloma bonded terms discrepancies

  #209 opened 9 months ago by laurenwinkler
  15

• Combining Espaloma and Amber

  #192 opened 9 months ago by amin-sagar
  5

• avoid pydantic 2

  #170 opened 9 months ago by chrisiacovella
  14

• error:KeyError: 'xyz'

  #208 opened 10 months ago by exYuan
  1

• Issues trying to reproduce atom typing recovery experiment

  #202 opened a year ago by rohithmohan
  3

• Simulation with 2 `espaloma` molecules explodes

  #205 opened a year ago by JSLJ23
  3

• Called setPositions() on a Context with the wrong number of positions

  #194 opened a year ago by hanboy315
  11

• Indexing error for two-atom molecules

  #191 opened a year ago by lilyminium
  2

• Question: what is the script used for training espaloma 0.3.2?

  #196 opened a year ago by pmorerio
  5

• Issue with conda installation

  #195 opened a year ago by pmorerio
  3

• Question about energy contributions related to "coefficients" in node features

  #197 opened a year ago by pmorerio
  0

• Called setPositions() on a Context with the wrong number of positions

  #193 opened a year ago by hanboy315
  3

• Throw an Exception if provided a molecule with elements that are not covered

  #190 opened a year ago by jchodera
  1

• Espaloma cannot use constrained (default) OpenFF force fields

  #189 opened a year ago by mattwthompson
  0

• qcportal 0.50 is incompatible with espaloma

  #185 opened a year ago by pavankum
  10

• Add docs on downloading new QCFractal datasets (or including your own) and building new force fields

  #146 opened 2 years ago by jchodera
  1

• Improved documentation on how to use local model

  #182 opened a year ago by ijpulidos
  2

• Charges are not reproducible when loading a pretrained model from disk file

  #181 opened a year ago by FloLangenfeld
  8

• Availability of benchmarking datasets from espaloma 0.3.0

  #180 opened a year ago by LeifSeute
  3

• Saving prmtop files from espaloma parameterization

  #145 opened 2 years ago by mmagithub
  4

• example "Deploy espaloma 0.2.0" breaks

  #158 opened a year ago by micaela-matta
  8

• Environment yaml file with explicit versions

  #147 opened a year ago by simonaxelrod
  3

• Fail to train on gen2 dataset

  #159 opened a year ago by Guackkk
  1

• Improve testing coverage

  #174 opened a year ago by ijpulidos
  0

• Add `get_newest_model` funtion

  #168 opened a year ago by mikemhenry
  2

• Add quick start to README

  #131 opened a year ago by mikemhenry
  1

• Switch to using Read the Docs

  #165 opened a year ago by mikemhenry
  3

• Charge Method Question

  #141 opened a year ago by madilynpaul
  4

• Add comment to why the input features were changed

  #162 opened a year ago by kntkb
  0

• Change default forcefield to latest openff

  #160 opened a year ago by ijpulidos
  2

• Docstring for sequential.py is outdated

  #150 opened a year ago by kntkb
  0

• Cannot change improper torsion multiplicity

  #156 opened a year ago by kntkb
  0

• Node featurization does not properly assign hybridization using OpenEye toolkit

  #143 opened 2 years ago by kntkb
  2

• Dataset splitting does not work as intended for some cases

  #149 opened 2 years ago by kntkb
  0

• Question: example code for setting up MD simulation of protein-ligand complexes

  #135 opened 2 years ago by mganahl
  1

• Nonbonded forces not properly subtracted from reference derivative

  #139 opened 2 years ago by kntkb
  0

• [Question] Evaluating Amber ff14SB and espaloma on Pepconf

  #138 opened 2 years ago by LeifSeute
  0

• [Question] Datasets for reproduction of the QM results in the paper

  #136 opened 2 years ago by LeifSeute
  1