ADL: Charges for AutoDock Vina

Ming Hao haom.niaid at gmail.com
Wed Oct 7 05:32:28 PDT 2020


Hi Gianluca,

Please have a look at this.

http://vina.scripps.edu/manual.html#faq

*Why don't the results change when I change the partial charges?*

AutoDock Vina *ignores *the user-supplied partial charges. It has its own
way of dealing with the electrostatic interactions through the hydrophobic
and the hydrogen bonding terms. See the original publication [*]
<http://www3.interscience.wiley.com/journal/122439542/abstract> for details
of the scoring function.

http://vina.scripps.edu/tutorial.html

Thanks,

Ming



On Wed, Oct 7, 2020 at 1:34 AM Gianluca Interlandi <
gianluca at u.washington.edu> wrote:

> Sorry, I need to correct. My receptor does not have charges from the
> CHARMM force field. The charges were generated automatically by ADT and
> they are Gasteiger charges. Is it OK to use Gasteiger charges for both
> receptor and ligand or should I use Kollman charges for the receptor for
> AutoDock Vina?
>
> Thanks,
>
>       Gianluca
>
> On Tue, 6 Oct 2020, Gianluca Interlandi wrote:
>
> > What charges shall I use for receptor and ligand in AutoDock Vina? Is it
> ok
> > to keep the charges that I already have for the receptor (generated from
> the
> > CHARMM force field) and Gasteiger charges for ligand? Or, do I have to
> use
> > Gasteiger charges for both, receptor and ligand?
> >
> > Thanks!
> >
> >     Gianluca
> >
> > -----------------------------------------------------
> > Gianluca Interlandi, PhD gianluca at u.washington.edu
> >                    +1 (206) 685 4435
> >                    http://gianluca.today/
> >
> > Research Assistant Professor at the Department of Bioengineering
> > at the University of Washington, Seattle WA U.S.A.
> > -----------------------------------------------------
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
>                      +1 (206) 685 4435
>                      http://gianluca.today/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>


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