stko

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Rewrite atom typer for UFF in Gulp.

5

Found issues with the handling of conjugation in stko.GulpUFF.assign_FF(). The method was written based on rdkit code, but the rdkit code also uses the bond order to set bond types,...

andrewtarzia

Calculate energy with orca Issue

1

**when using the below code:** ```python orca = stko.OrcaEnergy(     orca_path='/home/cmja2/orca',     output_dir='./Polymer2_ORCA',     topline='! SP B97-3c',     write_input_only=False,     discard_output=False, ) orca.get_results(polymer) ``` **this error occurs:** ```   File "/home/cmja2/anaconda3/lib/python3.11/site-packages/stko/_internal/calculators/orca_calculators.py", line 202, in _check_outcome     if...

Joe-Anslow

https://github.com/JelfsMaterialsGroup/stko/blob/3cb09caee41aff33349f82e375f9a8611565f0d8/src/stko/_internal/optimizers/collapser.py#L796

lukasturcani

``` $write gbsa=true ``` in `_write_detailed_output`.

andrewtarzia

https://github.com/cclib/cclib

andrewtarzia

Use the calculate_rmsd tool with the Kabsch algorithm. Actually just use this tool: https://github.com/charnley/rmsd/tree/master/rmsd

andrewtarzia

STKO fails for xTB conda version, not compiled version

1

victorhph8

for opts and MD? https://notebook.community/open-forcefield-group/openforcefield/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark

andrewtarzia

This is from a discussion with @lihaoran-001, where on HPC machines it might be useful to be able to specify where the GULP library files are kept directly in stko....

andrewtarzia

I have found many examples of structures after UFF4MOF optimisation or high T MD (using Gulp through stko), where H atoms near binding sites will be pointing the wrong way...

andrewtarzia