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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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How to process docking with two Cu ions? #205

Open pharm-dacnhan opened 1 year ago

pharm-dacnhan commented 1 year ago

We are doing a project related to tyrosine kinase protein, in which we need process the docking step with 2 ions Copper instead of zinc. Thus, we need to modify the file AD4Zn.dat. We added the parameter of Cu (atom_par Cu) with Rii, epsii, vol, and solpar values of 3.50; 0.005; 12.000; and -0.00110. Then, we process Docking. I wonder if this action is correct? We appreciate for any comments from experts. Many thanks!

diogomart commented 1 year ago

Yes, but I'd use a vdW radius more similar to that of the other metals.

xavgit commented 1 year ago

Hi, inspecting the AD4Zn.dat file there are lines for Mg, Ca and other metals different from Zn. Therefore to make a docking involving a metal present in AD4Zn.dat it is sufficient to follow the steps in the tutorial "Docking with zinc metalloproteins"? I can use the command; pythonsh /zinc_pseudo.py -r protein.pdbqt -o protein_tz.pdbqt even in the case of metal that is different from zinc?

Many thanks. Saverio

diogomart commented 1 year ago

Hi,

If there's no Zinc then there's no need to follow the AD4Zn instructions, the regular docking tutorial suffices, because the AD4Zn.dat file does not add any metals that aren't already included in the hard-coded defaults.