UCL-CCS/TIES

Issues

• Huge tiime-consuming at pair.superimpose

  #332 opened 4 months ago by ytworks
  0

• Stereoisomerism

  #331 opened 8 months ago by AlexW12344
  4

• Charge assignments with antechamber

  #330 opened 9 months ago by AlexW12344
  3

• use_element_in_superimposition

  #329 opened 10 months ago by AlexW12344
  3

• TIES with OpenMM

  #328 opened 10 months ago by Oulfin
  3

• ties_ana FEP method

  #322 opened 10 months ago by Oulfin
  1

• Super impose ligands issue with oxazole,thiazole, and imidazole

  #323 opened 10 months ago by Oulfin
  4

• Prepping Thrombin to reproduce TIES paper

  #326 opened a year ago by AlexW12344
  4

• Odd topology with CDK2 l20-l21

  #324 opened a year ago by adw62
  9

• Visualization, run single LAMBDA folder, and extension of simulations

  #320 opened a year ago by Oulfin
  2

• Speed/performance OpenMM with CDK2 example

  #318 opened a year ago by Oulfin
  7

• Fluorination workflow no longer working

  #319 opened a year ago by adw62
  3

• OpenMM input details

  #317 opened a year ago by Oulfin
  2

• Examples of Protein residue mutation?

  #316 opened 2 years ago by aminsagar
  4

• Do not require renaming uniquely atoms to generate an alchemical .pdb file

  #305 opened 2 years ago by bieniekmateusz
  0

• Using OpenMM for test cases and single point energy calculation in CI

  #293 opened 2 years ago by bieniekmateusz
  0

• Ambertools 22.0

  #291 opened 2 years ago by bieniekmateusz
  0

• A reason for the removal of an atom pair: dictionary

  #278 opened 2 years ago by bieniekmateusz
  0

• Switch to Jinja templating engine for the TIES20 input files

  #279 opened 2 years ago by bieniekmateusz
  0

• Test renaming of atoms is considered with manual unmatching

  #280 opened 2 years ago by bieniekmateusz
  0

• Smart netqtol feature - copying of suptop does not resolve all details properly?

  #264 opened 2 years ago by bieniekmateusz
  0

• Test cases: create test cases for the removal of atoms due to different reasons (united_charge)

  #271 opened 2 years ago by bieniekmateusz
  0

• Make logging clearer - mention how the symmetrical superimpositons are resolved

  #276 opened 2 years ago by bieniekmateusz
  0

• Check why the .namd input files are not copied

  #277 opened 2 years ago by bieniekmateusz
  0

• Add to the analysis module: Kendall's tau

  #247 opened 2 years ago by bieniekmateusz
  0

• Charges done before disjointed components

  #251 opened 2 years ago by bieniekmateusz
  0

• Automate gathering attributes from argparse directly into config into a single line

  #254 opened 2 years ago by bieniekmateusz
  0

• The fourth rule when the CCs are of the same size

  #259 opened 2 years ago by bieniekmateusz
  0

• Ignore hydrogens in the superimpositions

  #261 opened 2 years ago by bieniekmateusz
  0

• Define debug mode and other modes

  #240 opened 2 years ago by bieniekmateusz
  0

• Add a new rule for Search Space Optimisation when the molecules are mostly rings

  #244 opened 2 years ago by bieniekmateusz
  0

• Antechamber bug: space in .mol2 converted into an atom

  #245 opened 2 years ago by bieniekmateusz
  0

• Prepare for the Lead Mapping Optimisation

  #236 opened 2 years ago by bieniekmateusz
  0

• Rename atoms before generating GAFF ff for the ligand

  #237 opened 2 years ago by bieniekmateusz
  0

• When creating dummy atoms for testing, use the general library to figure out the atom type

  #238 opened 2 years ago by bieniekmateusz
  0

• Start moving into python properties

  #239 opened 2 years ago by bieniekmateusz
  0

• Improve the mapping of atom names

  #234 opened 2 years ago by bieniekmateusz
  0

• Add TIES_MD tests.

  #310 opened 2 years ago by adw62
  0

• NAMD estimators

  #296 opened 2 years ago by adw62
  0

• HETERATOMS cause NAMD issues

  #306 opened 2 years ago by adw62
  3

• command line wrong alchemical indexes

  #304 opened 2 years ago by adw62
  7

• Spurious bonds since ParmED update

  #302 opened 2 years ago by adw62
  16

• leaprc.protein.ff19SB: not found

  #303 opened 2 years ago by adw62
  3

• MD Analysis mol2 files

  #297 opened 2 years ago by adw62
  5

• pyqcprot N < 2

  #299 opened 2 years ago by adw62
  3

• Ligands prepped with Maestro

  #284 opened 2 years ago by adw62
  6

• Mached atom exception

  #295 opened 2 years ago by adw62
  3

• Constraint files for arbitrary water models

  #289 opened 2 years ago by adw62
  3

• Use dihedral angles to distinguish between different stereochemistry

  #283 opened 3 years ago by bieniekmateusz
  6

• ties20 - ties_md code duplication

  #285 opened 3 years ago by bieniekmateusz
  0