I am now using Autodock Tools and Autodock 4 to figure out the interaction of ligand-protein.
However, there is a problem I have to face now is that the Zn in the protein has 0 charge instead of +2 charge
How I can add charge in to this atom using Autodock 4 PROCEDURE?
Spending much time on this but still not figure out. Im hopeful of your help. Thank you.
Use this "AD4.1_bound.dat" file. It has the parameter for zinc directly.
http://autodock.scripps.edu/resources/parameters/AD4.1_bound.dat/view
Hi Ta,
You should modify the charge from 0.0 to +2.0 in your pdbqt file using text editors like WordPad.
Thank you Mr Yoshinobu Ishikawa. After changing charge of Zn, should I dock by Autodock Vina or Autodock 4? I have heard that Autodock Vina can not calculate ligand-metal ion interaction.
Im really looking forward to hearing from you soon. Thank you Yoshinobu Ishikawa
Ta Khanh Thi One better suggestion could be use, AutoDock Vina than AutoDock to overcome this error.
You should use AutoDock 4, because AutoDock Vina does not handle metalloproteins well.
Or, I recommend trying idock, which can handle many metalloproteins and dock ligands very quickly:
https://github.com/HongjianLi/idock
https://github.com/HongjianLi/idock/releases
You can use the same configure file as AutoDock Vina.
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