Diogo

The second picture looks like protein sidechains, but the first one does not. I don't think one is the output of the other.

There is no ligand in the second picture.

There is one difference in the implementation that I know of (there might be more). It has to do with H-bonds. In AutoDock4, AutoDock-GPU, and Vina with AD4 scoring, the...

Hello, Vina doesn't read the .dat file, the only thing that can be done is changing the type to something vina recognizes, such as Fe. Vina treats all metals the...

It would be quite some work, the code is designed for pairwise interactions.

Hello, Thanks for reporting, this is unexpected, I'll try to reproduce the behavior in my next screening. A comment on the grid maps: 0.5 A spacing is too coarse, I...

Yes, that can be useful. Thanks!

Ok. Thanks. Let us know.

Maybe [meeko](https://github.com/forlilab/Meeko) can help, see [docking covalent ligands as flexible sidechains](https://github.com/forlilab/Meeko#docking-covalent-ligands-as-flexible-sidechains).

There's no way to define new types or read in a parameter file. There's only the `--derivtype` option that you described. However, this may help: https://github.com/ccsb-scripps/AutoDock-GPU/wiki/Anchored-docking