ADL: Zero Charge Warning in DNA

Susantha Ganegamage susanthakgg at gmail.com
Sun Apr 26 11:10:19 PDT 2020


Hi,


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
format.


  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: https://doi.org/10.1002/cmdc.201300288,
https://doi.org/10.3390/molecules181012051)


Thank you and best regards,


Susantha Ganegamage


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