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openforcefield / protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations
MIT License
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Investigate clashes #73

Open IAlibay opened 1 year ago

IAlibay commented 1 year ago

The following clashes were identified by @dotsdl

cmet:
- lig_CHEMBL3402745_200_5
- lig_CHEMBL3402745_200_5

hif2a:
- lig_224
IAlibay commented 1 year ago

hif2a's lig_224 "clash" is a 0.79 A overlap between atoms O25 and C27. See below for weird geometry.

image
IAlibay commented 1 year ago

@dotsdl I'm unable to reproduce the clash you identified for cmet, visual inspection seems fine, could you double check here?