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.
I'm trying to add OH⁻ in a water box, but I can't generate the .inpcrd and
.prmtop. I'm sending in attachment the files I'm using and the file with
the output that I get.
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- application/octet-stream attachment: tleap.out
- application/x-aportisdoc attachment: oh.pdb
- application/octet-stream attachment: tleap.in
- application/octet-stream attachment: na.pbd
Received on Sun Oct 13 2019 - 11:00:02 PDT
