MobleyLab/FreeSolv

Issues

• Is gromacs_energies available to download anywhere?

  #52 opened 2 years ago by xiaowei-xie2
  4

• mobley_3323117 (sulfolane) has non-standard SMILES

  #51 opened 2 years ago by jchodera
  1

• gromacs-mdp:with verlet lists rcoulomb!= rvdw is not supported

  #49 opened 3 years ago by yuchen22
  3

• Sanitize SDF files

  #48 opened 4 years ago by proteneer
  0

• Problems with processing some SMILES - omega returned error code 0

  #47 opened 5 years ago by kadiliissaar
  0

• rebuild_freesolv.py script

  #46 opened 5 years ago by kadiliissaar
  2

• Cannot generate GAFF mol2 from Tripos mol2 file

  #45 opened 5 years ago by jchodera
  2

• GAFF version

  #44 opened 7 years ago by nhenriksen
  5

• Potential duplicate molecules in FreeSolv Set

  #40 opened 7 years ago by bannanc
  12

• Set up Travis-CI testing

  #42 opened 7 years ago by davidlmobley
  0

• Re-generate trajectories for all compounds - implicit solvent, explicit solvent, and vacuum

  #15 opened 7 years ago by davidlmobley
  3

• Have GBSA models been benchmarked on FreeSolv?

  #24 opened 8 years ago by jchodera
  4

• Make CHARMM input files via ParmEd

  #35 opened 8 years ago by davidlmobley
  0

• Update column names to be more informative

  #33 opened 8 years ago by jchodera
  2

• Should SDF files contain other fields from database?

  #14 opened 10 years ago by jchodera
  2

• Naming convention for 'title' record in Tripos mol2 files

  #13 opened 8 years ago by jchodera
  5

• Flag molecules with possibly problematic tautomers (and investigate tautomers for them)?

  #29 opened 8 years ago by davidlmobley
  0

• Decide any other supporting files/data which ought to be captured when database is re-constructed from primary data

  #19 opened 8 years ago by davidlmobley
  2

• Resolve issues relating to trajectory re-generation and re-calculation of hydration free energies

  #17 opened 8 years ago by davidlmobley
  1

• Re-compute hydration free energies for all compounds

  #16 opened 8 years ago by davidlmobley
  1

• Re-construct database files from primary data

  #20 opened 8 years ago by davidlmobley
  11

• Strip water molecules from all topology/coordinate files in current database

  #21 opened 8 years ago by davidlmobley
  8

• Protocol for generating solvated input files for various codes (AMBER, gromacs)

  #22 opened 10 years ago by jchodera
  1

• In next update, include a json format version of database

  #27 opened 8 years ago by davidlmobley
  1

• Migrate issues and close this repo?

  #25 opened 8 years ago by davidlmobley
  10

• mobley_352111 and mobley_4689084 are the same molecule

  #6 opened 10 years ago by leeping
  9

• Implement Bayly's recommended AM1-BCC charge assignment scheme

  #12 opened 10 years ago by jchodera
  0

• Add source for v0.31_docs.pdf

  #2 opened 10 years ago by jchodera
  6

• Add scripts used to generate these files

  #3 opened 10 years ago by jchodera
  6

• Decide what additional data we want pulled from the source literature/what instructions to give

  #18 opened 10 years ago by davidlmobley
  0

• Which database format should store primary data?

  #9 opened 10 years ago by jchodera
  2

• Create Release for v0.31

  #8 opened 10 years ago by jchodera
  3

• Delete ANTECHAMBER.AC file in top directory?

  #1 opened 10 years ago by kyleabeauchamp
  4