Unknown atom type

[Teohoho]

Hello! I attempted to run a docking simulation using AutoDock-GPU, v1.5.3-24 and I get the following error:

Error: Ligand includes atom with unknown type: Pt.

I have used a parameter file to explicitly define the parameters for Pt, Se and B, and added the corresponding line into my .gpf file prior to generating the map files and I successfully generated them. However, when running the actual docking simulation, it stops and returns the above error, along another one that reads:

Error: Could not identify ligand atom type Se.

My ligand set includes molecules with these metals, alongside Boron, which works, despite not being in the default parameter set.
Thank you.

[diogomart]

Hello,

AutoDock-GPU does not read the parameter file. Boron has been included recently. It may be reasonable to replace Selenium with Sulfur, and it is possible to do this with -T Se=S, which will treat Se as S for direct interactions: ligand-ligand, and ligand-flexres.

[Teohoho]

Thank you for the quick reply! So there is currently no way to manually add parameters for other elements, such as Platinum?

[diogomart]

Hi, sorry, forgot to reply. Unfortunately there isn't.