Hi everyone I am attempting to prepare a ligand-protein complex for AutoGrid flexible docking simulations, using AutoDock Tools.
I am using the 5HT1B-ergotamine crystal complex (codename 4IAR on RCSB). I selected and deleted the ergotamine molecule, and I'm attempting to introduce my own ligands for binding studies on the receptor.
I am using this video as a guideline: https://www.youtube.com/watch?v=ZiuqSzqcD7M
In the video, at roughly 10:30 in, the instructor goes under Grid>Set Map Types>Set Up Covalent Map. He then selects an amino acid residue on the protein receptor--specifically, Serine-195--and alters the program settings.
I was wondering if anyone could possibly tell me (or link me a tutorial) on how to properly set up covalent grid parameters on my receptor protein of choice? This is apparently designed to accommodate ligands which form covalent bonds on the receptor. Is it possible to determine this myself or do I need empirical evidence/data concerning the binding affinity of ligands to the 5HT1B receptor?
Or better yet, is it possible to use the original ligand-protein complex (5HT1B and ergotamine) to determine where covalent bonds are likely to form?
Cheers and best regards
I have same issue could anyone please explain the solution for this problem as mentioned above.?
Aaron Dumont did you find out? I'm using that video too, so if you came up with the solution, please let us know
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