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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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Unknown atom type #190

Closed Teohoho closed 2 years ago

Teohoho commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

diogomart commented 2 years ago

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