[Zinc-fans] Zinc 7 and partial charges

[John J. Irwin]

Hi John

John Doe wrote:
>
> Dear Zinc-fans,
>
>  A simple question: are the partial charges already assigned to the 
> compounds in Zinc7 suitable for Autodock? in other words, should 
> partial charges reassigned before performing a virtual screening using 
> AutoDock 4?
The charges in ZINC 7 (all versions from 6 on) are AMSOL AM1 SM5.42R 
charges using AMSOL 6.5.3 as per Wei BQ et al. J. Mol Biol. 
322(2):339-55 (2002) based on a single Corina-generated (gas-phase) 
conformation.

In my view they are reasonable charges to use for any physics-based 
scoring function. I would not want to argue that you couldn't do better, 
but they are the charges we continue to use to this day. As with all 
calculations, we counsel retrospective controls to recapitulate 
experimental data prior to making prospective predictions.

Good docking!

John,  http://johnirwin.docking.org/
UCSF ZINC Team, http://zinc.docking.org/

>
> Thanking you,
>
> John Doe
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