Rocco Meli

Interestingly, [https://open-babel.readthedocs.io/en/latest/index.html](https://open-babel.readthedocs.io/en/latest/index.html) seems to still point to 3.0.1 despite the current version being 3.1.1

I believe this is liked with Issue #1336 and PR #332.

When inverting the `ENDMDL` and `END` cards (as in the output of an old version of `smina`, using OpenBabel 2.3.90), everything works fine. Since `smina` output is based on OpenBabel,...

The following format ``` MODEL ENDMDL MODEL ENDMDL END ``` seem to work correctly, but the following error is nonetheless printed: ``` ============================== *** Open Babel Error in ReadMolecule ERROR:...

Yes, I was planning to open one in the next few days if this the idea was OK. I'll leave this open as a reminder.

Hi, thank you for reporting the issue. Can you please provide more details on how you perform the docking and the re-scoring? I can't reproduce your issue (tried with one...

As @dkoes mentioned, in order to get the same results when re-scoring the docked pose you need to include the same flexible residues (in order to include the same intramolecular...

If you want to minimise with Gnina, you also need to set the `GNINA_CMD` variable to point to your Gnina executable, see PR #26

https://github.com/mattragoza/liGAN/blob/7d760bde1c94d755113c05849fb81b905888fb1b/fitting.py#L618-L627 A possible solution is to use `max(pt.GetValenceList(a1.GetAtomicNum()))` instead of `pt.GetDefaultValence(a1.GetAtomicNum())`. I can open a PR if this is of interest.

> Or could we do even better by assuming a small size for the vector and using a fixed size container with a linked list tacked on. Not sure if...