Re: [AMBER] Query about adding hydrogens

From: Bill Ross <>
Date: Sat, 11 Jul 2015 15:20:41 -0700

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.


<div>-------- Original message --------</div><div>From: anu chandra <> </div><div>Date:07/11/2015 1:08 PM (GMT-08:00) </div><div>To: AMBER Mailing List <> </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

AMBER mailing list
AMBER mailing list
Received on Sat Jul 11 2015 - 15:30:02 PDT
Custom Search