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
