[AMBER] Adding OH- to a water box

From: David Case <david.case.rutgers.edu>
Date: Sun, 13 Oct 2019 12:16:49 +0000

On Sat, Oct 12, 2019, Lucas Bandeira wrote:
> > Why is it not as easy as adding water with AddToBox? You just define a
> > PDB file with two atoms (for the OH molecule), and use AddToBox in the
> > usual way. I do that all the time for molecule ions.
> But what about the overall negative charge in the OH⁻? It will be add
> automatically?

AddToBox just uses size considerations, and doesn't try to evaluate
electrostatics. The charges on the atoms will be in the unit you create
(usually in mol2 format, but possibly in prep or off formats) that you
will then load into tleap.


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Received on Sun Oct 13 2019 - 05:30:02 PDT
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