ADL: Zero Charge Warning in DNA

Van Dam, Hubertus hvandam at
Sun Apr 26 14:57:49 PDT 2020

Hi Susantha,

The docking score involves multiple terms, including an electrostatic term. To evaluate the electrostatic term you need to have charges on the atoms. Note that the PDB format does not allow for atomic charges. So when you generate the PDBQT files you need to add those charges (alternatively you may generate PDBQT files from MOL2 files which can accommodate charges). There are multiple ways of calculating atomic charges, one program that can do that is OpenBabel. However, any basic tutorial should describe the need to add charges and provide some recommendations on how to do this. As different algorithms for calculating charges will provide different answers it is usually best to use those charge models for which the docking score has been calibrated.

Best wishes,


Hubertus van Dam, 631-344-6020, hvandam at
Brookhaven National Laboratory

On 4/26/20, 14:11, "autodock-bounces at on behalf of Susantha Ganegamage" <autodock-bounces at on behalf of susanthakgg at> wrote:

    I tried to prepare a DNA molecule (PDB ID: 3CE5) for docking. I deleted
    water and then ligand molecule (BRACO19). Then, I saved the DNA molecule as
    PDB format. After that, I select the molecule using
    Grid--->Macromolecule---->select 3CE5------>Select Molecule-----> OK.
    The following error the message came when I try to save this file in .pdbqt
      WARNING: These  atoms have zero charges: O5’ K K O6
    How do I solve this problem? I can’t run autogrid or autodock with this.
    But I saw in the literature people have done docking with this molecule.
    (References:;!!P4SdNyxKAPE!THfmcxWdyaJOdY5XZsMAxsPb218JvGmHDzbhWe22EB7HzvpttHjwx7dViKo_rys$ ,;!!P4SdNyxKAPE!THfmcxWdyaJOdY5XZsMAxsPb218JvGmHDzbhWe22EB7HzvpttHjwx7dVyhCeF_I$ )
    Thank you and best regards,
    Susantha Ganegamage
    --- ADL: AutoDock List  ---;!!P4SdNyxKAPE!THfmcxWdyaJOdY5XZsMAxsPb218JvGmHDzbhWe22EB7HzvpttHjwx7dVOI-yuCA$  ---

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