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 Post subject: Partial Charge of Ligand
PostPosted: Wed May 06, 2015 9:44 am 
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Joined: Wed Jan 08, 2014 7:40 am
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I want to ask about partial charge of ligand. Before we run the molecular docking simulation, we will run the preparation of the ligand and save it in pdbqt file. If I read some paper, it is said that partial charge of atoms is important related to binding affinity and interactions.
As I know, in autodock, usually partial charge of ligand are computed using Gasteiger method. But it gives so many different with partial charge that I compute with DFT method using Gaussian software. But, I'm not sure to directly change the pdbqt file because it doesn't compute partial charge of non-polar hydrogen so the total charge is different with the actual one.

So, is there any suggestion or opinion, which is better for doing molecular docking simulation, using partial charge directly from Autodock or I change by myself based on DFT calculation? Because I found it gave so many differences.

Thank you for your help and for your suggestion.


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