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openforcefield / protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations
MIT License
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Investigate abnormal ligand conformations in CDK8 #72

Closed IAlibay closed 1 year ago

IAlibay commented 2 years ago

Ligands 22, 29, 30, 32, 36, 38, 39, 43, and 45 appear to have abnormal (squashed) ring conformations for CDK8 (see attached for examples).

Whilst these should all minimize out, it would be good to work out what remedial actions (if any) should be taken to avoid these.

image

IAlibay commented 1 year ago

Should be fixed now.