AutoDock does not have forcefield parameters for most ions and metals ions. You have to manually add the parameters to get your docking done successfully.
Below are the parameters for As
atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
You just need to append above line in your ADT4.1 [or current version]_bound.dat file. Then use this file for docking instead of the file given by default.
Follow this tutorial for more details :
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
I hope it solves your problem.
Dear Kundu,
The same question was answered here
https://www.researchgate.net/post/How_to_perform_protein_docking_with_metal_ions_using_autodock.
Also, you can use MIB (http://bioinfo.cmu.edu.tw/MIB/) docking tool alternatively, or there are few more tools.
Dear Dr. Pal,
May you please suggest some software and protocol that I can use for this process?
Dear Dr. Naqvi,
THank you for the info. I have got another set of published parameters which I can refer for Arsenic. Thank you so much.
Dear Dr. Ahmad,
Thank you for the MIB link. However, it has a limited set of metal ions that can be checked for interactions.
Soumya Kundu I would suggest Desmond. The system is easy to set up and the OPLS force field that comes with Desmond contains parameters for almost all he elements in the periodic table. You may refer to the following article:
Article Metal Ions Provide Structural Stability and Compactness to T...
Although we have used Ca2+ and Mg2+ in this article, similar protocol maybe used for As3+. However, free As3+ ions probably do not exist in solution and covalent compounds (AsCl3, AsO33- etc.) should be used, instead.
https://www.chem.uwec.edu/chem491_w01/Chem491-Molecules%20and%20Medicine%202008/AutoDock%20Tutorial.pdf
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