search

MobleyLab / benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
BSD 3-Clause "New" or "Revised" License
42 stars 16 forks source link

fix bonds and protonation for BRD4 ligand 5 #74

Open GHeinzelmann opened 3 years ago

davidlmobley commented 3 years ago

For posterity, can you explain what you're correcting and why?

Also, were the reported calculations affected?

GHeinzelmann commented 3 years ago

Hi. I made the change suggested by David Huggins, which was changing the NAL-CAO bond to a double bond on ligand 5 from the BRD4 set, thus also removing two hydrogens from this molecule. There were no free energy calculations performed for this particular ligand, it was only added to the benchmark as a model system.