How can i dock my ligand with a cofactor in AutoDock?

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

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Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

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Martin Klvana

Make the cofactor a part of the receptor.

Anas Alobaidi

can you explain more about your cofactor?

is it like ZN?

Michiel Vanmeert

You could try to make the cofactor a part of the receptor as suggested before but this usually results in problems with the torsion definition. If you have access to it, you could try the recently implemented AMBER docking which readily puts you in a well characterized and widely-used forcefield.

Abeeb Abiodun Yekeen

Hi Atam Noyan Erçetin

What cofactor? If it's Zn, you can use AutoDock4Zn.

However, you can check this paper (link below) on the evaluation of the performance of seven docking tools in metalloprotein docking:

Article Comparative Assessment of Seven Docking Programs on a Non-Re...