Diogo

The `score()` function does only a single point energy evaluation using the input coordinates. To dock the ligand you need to call the `dock()` function. The error was added to...

> No, I call dock() just like the script in docs. But with vina 1.2.3, I have to increase box size to 200x200x200 to bring ligand inside the box. This...

In your script you are calling `score()` before calling `dock()`. At that point, its position and orientation are independent from the protein, so it's not surprising it is outside the...

What do you mean by "without the config file"? Any option can be either in the config file or passed as a parameter. The `--score_only` or `score()` calculate the energy...

@FeiLiuEM could you post the contents of the `.gpf` file?

We are working on receptor preparation. There's a recently developed and feature-incomplete `mk_prepare_receptor.py` in [meeko](https://github.com/forlilab/meeko), currently in branch "reactive" but should be released as v0.5.0 soon. This script strictly requires...

See #204 for how to handle flexible sidechains on a rigid cyclodextrin core. Also, it should be possible to use [meeko](https://github.com/forlilab/Meeko) to prepare the cyclodextrin as a flexible ligand, which...

@alchymy does this help? https://github.com/forlilab/tutorials/tree/main/installation-mac#vina-executable

@alchymy if you don't add `.dylib` extension and you execute `./vina_1.2.5_mac_x86_64` what does it print?

Are scores different for the first pose, or only from the second and subsequent poses?