benchmarksets
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MobleyLab
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
## References: - [ ] Read Lindorff-Larsen, Miao papers on lsozyme binding; include references and relevant insights. Lindorff-Larsen reference: https://elifesciences.org/articles/17505 - [ ] Reference Pan paper: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00172 - [ ]...
example, butylammonium: https://github.com/MobleyLab/benchmarksets/blob/master/input_files/cd-set1/sdf/guest-1.sdf
@mkgilson I've uploaded in this branch the receptors in PDB format and ligands in mol2 format. The receptors are clean (no crystal waters) and they went through MCCE to obtain...
Can we add Markdown tables for the CB7 and GDCC sets like we have for the CD sets? Those are really helpful. I realize this information is in the manuscript...
@nhenriksen - we were trying to work with the cyclopentanol (guest 4) example from CD set 1, and noticed that the AMBER prmtop file has mixed 1-4 scaling factors (SCEE)....
I just want make sure you've noticed this issue ParmEd/ParmEd#898 . Briefly, manipulating the cyclodextrin `mol2` files with `parmed` results in a ring breaking. A work-around would be assigning a...
I think we should probably move towards a model where all ligands (or guests) in each benchmark set have an appropriate, unique, paper-specific numerical compound ID, rather than the current...
The CB7 and GDCC guest input files do not have coordinates which correspond to a bound state in the host. Per Niel: > They are close [to bound], but clearly...
To move this in the direction of helping people benchmark, we should provide calculated values from gold standard calculations with the provided files, when available. These should be in a...