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Using XTB built-in constraining potentials for metal / ligand binding #4

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7 of 10 tasks
joshkamm opened this issue Apr 13, 2022 · 0 comments
Open
7 of 10 tasks

Using XTB built-in constraining potentials for metal / ligand binding #4

joshkamm opened this issue Apr 13, 2022 · 0 comments
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joshkamm commented Apr 13, 2022 •
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Notes from simplification of metal-ligand binding using XTB built in biased optimization instead of GSM, as well as some other cleanup and refactoring.

  • go through main.cpp and clean up commented out code
  • test with phosphine literature ligands
  • After binding, sort conformers by energy to see the ostensibly most realistic first
  • Extend workflow from debugging in vscode to running in a slurm job
  • Try test using full xTB instead of FF for quick debugging
  • Use IQMol to generate Pd(CH3)2 for testing binding
  • Test binding to Ph(CH3)2
  • Debug why first conformer doesn't seem to be performing alignment
    • may be a conformer getting carried over in main.cpp line 191
  • Execute on test ancillary ligands
  • automatically generate xtb.inp file
@joshkamm joshkamm self-assigned this Apr 13, 2022
joshkamm added a commit that referenced this issue Apr 13, 2022
@joshkamm
wip #4
40d0bc3 
added support for using XTB built-in constraining potentials for metal /
ligand binding instead of relying on GSM

refactored a number of functions to consolidate molecule data being
passed around into openbabel molecule objects

added (bool) casts to getline calls for newer compiler compatibility
joshkamm added a commit that referenced this issue Apr 27, 2022
@joshkamm
wip #4 clean up code, add phosphine test ligands
1d3f7fe 
test phosphine ligands taken from literature
joshkamm added a commit that referenced this issue May 4, 2022
@joshkamm
wip #4 update test ligand
65cd2fd
joshkamm added a commit that referenced this issue May 7, 2022
@joshkamm
wip #4 sort conformers by energy
7b78363
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