ADL: Determining total charge of a DNA molecule

Matt K mketterbob at gmail.com
Wed Mar 30 14:27:04 PDT 2016


I think you may be able to generate charges through different molecular
viewers, try Avogadro, jmol, or pymol.

On Wed, Mar 30, 2016 at 3:09 AM, dr. sakura <lalehan.ozalp at gmail.com> wrote:

> Hello, I'm working with DNA and a molecule I've been interested for a
> while.
> I ran docking numerous times and got valuable results. However, I feel the
> urge to optimize the DNA as well, apart from my ligand. I have the pdb
> crystal structure and I want to optimize it (through Gaussian or Spartan).
> The problem is, I exactly have to know the total charge before starting the
> job. I don't rely on just counting the phosphate groups or so. I looked for
> a module in Autodock, but couldn't find anything helpful yet. Does anybody
> have any idea how to overcome this?
>
> Thank you in advance.
>
>
>
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