I want to perform docking of arsenic with a protein. However arsenic is not present in the autodock parameter file I have added it and saved as .dat file. I don't know the procedure further. Can some one please help me with this?
Hi Shraddha Mishra ,
Here is the step-by-step video link (http://vina.scripps.edu/tutorial.html)
Thanks for all the answers. I am using autodock vina and getting following message while running-
Dear Shraddha Mishra
As Arsenic is a single atom the correct word would be how to "bind" it to a protein because "docking" is a more complex process applied to a molecular ensemble, docking programs might give you an answer, but the binding of a metal to a protein would require a different approach than docking.
For a metal binding to a protein, there will be many putative binding sites, wherever you find a negative charged cluster, and more specially for multivalent metals an arrangement of bases like histidine, many metals are also bound to water molecules to satisfy and stabilize their coordination state.
My questions for you is if you know for a fact that your protein binds Arsenic or another metal that could be replaced by Arsenic, or you are theoretically exploring the possibility ?
Before starting any in-silico experiment bout metal binding I would always ask the experimentalists to detect the fact that a metal is bound and give me if they can an estimate of the binding energy, then I would go and perform a very serious study of the possible binding sites and use a combined approach, possibly using DFT (Density Functional Theory) to model them ..
Cheers,
Rolando.
Thank you so much for the suggestion. I am using a protein that is known to bind arsenic in other bacterial species. I don't have so much idea of how to perform metal and protein binding study. It would be very nice of you if you can explain me from the basics.
I was able to run the autogrid4 command successfully and MAP files were generated but while running autodock4 command I am getting this error.
C:\Users\Hp\Desktop\workspace>autodock4.exe -p 2.dpf -l 2.dlg
autodock4.exe: FATAL ERROR: Sorry, I can't find or open AD4_parameters
autodock4.exe: Unsuccessful Completion.
Can someone please share me video tutorial or screenshots of how and where to add parameter file (with added arsenic) while generating .gpf file and .dpf file.
- Badges
- Science topic
- Similar topics
- Filing