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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Mg ions in a polymerase #108

Open Jameel9 opened 2 years ago

Jameel9 commented 2 years ago

Hello Sir

Can I use Vina to dock analogues of nucleotides triphosphates into a polymerase active site coordinating Mg ions? The ions are also typically in coordination with water molecules to satisfy their proper geometry. Is it possible to do such docking while, at least, Mg ions are kept at the active site?

eereenah-fast commented 2 years ago

Hello! Following up on this issue with the same question!:)

Jameel9 commented 2 years ago

@eereenah-fast You can actually.. Just rename the atoms in the pdbqt files from HETATM of Mg to ATOM and give it a try.

eereenah-fast commented 2 years ago

Thanks for the reply!

RJ-Li commented 11 months ago

I have an important question to ask you: How did you process the numerous pdb files which have ions such as Zn in the dataset in to pdbqt? I find they cannot be converted into PDBQT files, but I DON'T wanna deal with them with AutoDockZn(this method might use different scoring function than vina scoring funtion, so I cannot categorize them into vina) according to your suggestion, should I just change those HETATM into ATM? That sounds incredible! I will have a try