Macrocycle screening: "CG0" ATOM syntax error with Meeko ligands

[HaleHasdemir]

Hello,

I am reporting an atom type compatibility issue between Meeko and Vina-GPU-2.1 during macrocycle screening.

The Problem:
Ligands containing macrocycles generate a CG0 is not a valid AutoDock type error.

Current Workaround:
Using --rigid_macrocycles in Meeko allows the job to run, but prevents proper sampling of the macrocycle poses.

Question:
Has there been any recent improvement regarding the support of these atom types in the GPU version, or is flexible macrocycle docking still restricted to the CPU-based Vina?

Thank you

[pjmartel]

I have the same problem. But looking at the Vina-GPU repo, it appears there has been no development in the last 2 years. I fear the project is dead...

[HaleHasdemir]

@pjmartel , I tried Autodock-GPU as an alternative and it handles macrocycles and is equally fast. So, Autodock-GPU might be our solution for now.

[DUTchecheche]

Vina-GPU is developed based on the old version of Vina (1.1.2), while the macrocycle molecular docking is a new feature in Vina 1.2.x. This is the reason.