Diogo

I can't see the attachment, could you upload it on the GitHub webpage? Also, you shared a link to unsubscribe from email notifications, I deleted that link.

These are errors from RDKit, they indicate a problem with the SDF ``` [14:08:32] Explicit valence for atom # 67 O, 3, is greater than permitted [14:08:32] ERROR: Could not...

Hi @jaketanderson I added an example script here: https://github.com/forlilab/Meeko/tree/reactive/example/cyclodextrin_flexible It is in branch "reactive" that will be merged soon and released as v0.5. This will change the API and I...

Hello, Macrocycles are made flexible by default in [meeko](https://github.com/forlilab/meeko) and there's nothing special to do on Vina's end . So, that's correct, following the basic docking tutorial will dock macrocycles...

Documentation updated in 0575dfa17c4d2480ec4a354ae808c4ed53fbae0f

I'll re-optimize with Gaussian and maybe run the DLPNO single point. I'll make that data available. This is a really nice dataset and the fully optimized geometries may be useful...

I'll use D3BJ. I never used the def2- basis sets but will definitely consider them. Thanks!

No, the Solis-Wets (SW) in AutoDock-GPU is far superior to SW of AutoDock4. I think the difference is the magnitude of the changes in the coefficients that define the conformation...

The energies should be very similar for the same pose.

I don't recognize that option name. Might it be `--only-cluster-leads` in meeko's `mk_export.py`? https://github.com/forlilab/Meeko/blob/3748b68edc4b7a0ecee90009499052bfca0d8ce1/scripts/mk_export.py#L45