first draft of prep complex workflow#1

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Commits on Apr 11, 2023

first draft of prep complex workflow

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Commits on Apr 24, 2023

WIP: updated preparation files

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Commits on May 2, 2023

wip... sorry trevor lol
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Commits on Jun 14, 2023

wip
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wip
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Commits on Aug 8, 2023

Commits on Aug 9, 2023

fix ligand Hs being split into second residue issue

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Commits on Apr 11, 2024

add partial charge assignment to workflow

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change prep_complex.py to use unconstrained FF

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add example files to run with prep_complex.py

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Commits on Apr 19, 2024

fix bug in charging code related to renumbering of atoms when offmol -> oemol conf gen -> offmol
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Commits on Apr 21, 2024

fix order of protein, ligand, solvent in gro file to be compatible with septop

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fix NA CL naming convention
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