Problems with Ruthenium

[sdevita7]

Hello!

I am trying to perform a docking with a molecule containing Ruthenium using AutoDock Vina (v. 1.2.3) and the vina scoring function but, despite adding the corresponding parameters in the AD4_parameters.dat file, it still returns the following error:

AutoDock Vina v1.2.3

Scoring function : vina Rigid receptor: 5mwq_clean_total_site_1.pdbqt Ligand: aziru.pdbqt Grid center: X 0.4 Y 6.45 Z -7.6 Grid size : X 13 Y 13 Z 13 Grid space : 0.375 Exhaustiveness: 64 CPU: 0 Verbosity: 2

PDBQT parsing error: Atom type Ru is not a valid AutoDock type (atom types are case-sensitive).

HETATM 7 RU1 UNK 900 -0.139 0.241 -0.320 1.00 0.00 0.380 Ru

Can you help me understand what I am missing?

[diogomart]

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 same. By the way, bugs have been fixed since v1.2.3, you should use v1.2.5.

[sdevita7]

Thank you!