ADL: Determining total charge of a DNA molecule

dr. sakura lalehan.ozalp at
Wed Mar 30 03:09:45 PDT 2016

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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