I want to make docking using Autodock and both receptor and ligand are proteins. i followed the usual steps of docking small molecule ligand but when I reach to docking step, an error message says "too many torsions and the maximum is 32" appears. How can i solve this problem?
Thanks in advance
You cant do protein-protein docking by using autodock, you can do it by using Haddock
You need to put your grid in the specific area where you think it'll happen the docking and you could try to reduce the Grid too.
Yes it’s free you can follow this link
https://bianca.science.uu.nl/haddock2.4/
break the molecule to be docked into several pieces, and dock each one separately. Then, look for docked conformations that would be consistent with the entire molecule. This method was used many years ago to dock two proteins using AutoDock.dock a small portion from one end of the molecule. Then, extend the molecule, holding the end rigid in the conformation found in the first step, and allowing the new extension to move. Continue this, adding pieces to extend the molecule until the entire molecule is docked. This method was used successfully for a study of peptides bound to antibodies.
Noha G Mohamed
ZDOCK is a free and useful tool for protein-protein docking. You can use the web-based version on the following link:
http://zdock.umassmed.edu/
As Khattab Al-Khafaji recommended, HADDOCK is a free and reliable protein-protein docking tool.
Please try HADDOCK and ZDOCK for tool for protein-protein docking.
Other Good tools are PatchDock for initial docking and FireDock for refinement at http://bioinfo3d.cs.tau.ac.il/PatchDock. For protein-peptide docking (your case) very good is FlexPepDock which is part of Rosetta package.
Auto dock is not suitable for docking of two proteins. Use haddock 2 web server..
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