> On Jul 11, 2015, at 4:08 PM, anu chandra <anu80125.gmail.com> wrote:
>
> 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?
>
There is no single correct answer. LEaP will add hydrogens, but in an unsophistIcated way. The Amber distrubution includes the reduce program that will explore more possibilites. We generally recommend that people use the pdb4amber script to prepare pdb files....this provides an easy way to run reduce and to varry out other common tasks.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 24 2015 - 08:00:03 PDT
