[AMBER] Amber and Domains Conformational Dynamics

From: mario <mario_aglialoro-amber.yahoo.com>
Date: Sat, 29 Feb 2020 19:00:01 +0000 (UTC)

 sorry fo hijacking the mailing list
I have a naive question about MD and AMBER:
my protein of interest has 2 domains  first one binds ATP and phosphorilates a residue on 
the second domain.
Structures are solved (many homologs) with both ATP and analogs, but the distance between the phosphorilable residue on
the second domain and ATP or analogs is kind of too long. I want to have a better picture of the interfaces between the two domains 
during the phosphorilation reaction.
My idea is to model an ATP analog inside the first domain with molecular docking and covalently link it to a residue next to my 
phosphorilable one or to a mutated phosphorilable residue.

Would the amber package be of any help here:
- bond lenght between ATP analog and covalently linked residue is not a real one, so amber will move the two domains closer during
  simulation to have the bond geometry fits the standard ?
- or should I move the two domais closer by hand till the ATP analog covalent bond sounds right and then Amber will clean out the 
clashes between  the two domains ?
- nones of the above (I am missing something about MD) and I should try in a different way ?

Thanks for your time any help would be appreciated

Mario Aglialoro
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Received on Sat Feb 29 2020 - 11:30:02 PST
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