Why not try having leap add the H's, minimize, and superimpose initial and before/after min models to see if there is any flipping.
Bill
<div>-------- Original message --------</div><div>From: anu chandra <anu80125.gmail.com> </div><div>Date:07/11/2015 1:08 PM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] Query about adding hydrogens </div><div>
</div>Dear Amber users,
I am working with protein model building. I am planning to do MD simulation
of crystal structure and three different models of same protein. I just
have a quick query here regarding adding hydrogen to the structure. Do I
need to worry about the residue flipping while adding hydrogen, which
usually been done with programs like MolProbity? Will it be correct if I
directly add hydrogen through Amber leap program?
Many thanks in advance
Anu
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Received on Sat Jul 11 2015 - 15:30:02 PDT
