Procedure of treating Fe2+ Ion

[biotechjs]

Thank you for this fantastic tool!

I'm trying to perform docking on a site with Fe (II), what would the recommended procedure of doing so?

I have tried to

• manually change the charge of Fe to 0, 1.4, and 2 in the pdbqt, but the result doesn't seem to be dependent on that number
• I am not sure if https://autodock-vina.readthedocs.io/en/latest/docking_zinc.html would be applicable here.
• The following link doesn't seem to work anymore
  • http://autodock.scripps.edu/faqs-help/faq/metal-charges
• I have read https://github.com/ccsb-scripps/AutoDock-Vina/issues/216 but https://github.com/forlilab/Meeko/pull/48 doesn't seem to be ready yet.
  • is there any makeshift method/instructions of doing so?

[diogomart]

Vina treats all metals as a H-bond donor, and partial charges are not used. The Vina scoring function is so simple that there's nothing special that needs to be done about metals.

[biotechjs]

thank you @diogomart ! Just curious, would it be worthwhile to try your other project autodock-gpu?

[diogomart]

It may be worth trying the AD4 scoring function, which can be done also from Vina with the --scoring ad4 option. Often, one scoring function outperforms the other, and we don't really know why. Note that partial charges matter for AD4 scoring. If you have a lot of GPU power and want to dock a lot of molecules, then AD-GPU could be very valuable. AD-GPU also implements the AD4 scoring function.

[biotechjs]

thank you very much @diogomart !