ADL: How do I set a covalent map on a receptor protein using AutoDock Tools?

sandra sandra at theindoleshop.com
Sun Mar 20 23:41:55 PDT 2016



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


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