[Dock-fans] charge method

Brian Fochtman brianfochtman at gmail.com
Thu Sep 19 08:21:22 PDT 2013


Hi Mary,

Dock will use whichever partial charges you place in the mol2 file.  Most
validation on DOCK6.6 has been performed using semi-empirical am1-bcc
partial charges.  In my experience the partial charge model used can
improve our ability to identify crystallographic ligand poses by ~3%.

Hope this helps,

Brian Fochtman


On Wed, Sep 18, 2013 at 11:06 PM, Mary Varughese <maryvj1985 at gmail.com>wrote:

> HI,
>
> Is there any way so that i can use the partial atomic charges (as mol2
> file)derived from gaussian calculation in docking? There is some difference
> in charges. It may affect the derived conformation of the complex from dock6
>
> Thanking you
>
> Mary Varughese
> Research Scholar
>
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>
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