ADL: Charges for AutoDock Vina

Rick Sheridan ricksher at gmail.com
Mon Oct 12 10:15:07 PDT 2020


As this question comes up frequently, even from myself before, shouldn't
the manual or some appropriate centralized source see an editorial update
to better emphasize that Vina ignores user-supplied charges?  I’ve gotten
this wrong before and I wrote a how-to on Vina docking.  A
better-emphasized update would save a lot of people a lot of heartache.

Something along the lines of ‘ML-based classification vs physics’  perhaps?

Cheers,
Rick

On Wed, 7 Oct 2020 at 3:34 PM, Ming Hao <haom.niaid at gmail.com> wrote:

> 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 ---
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> --
-- 
********************************************************************
Rick Sheridan
********************************************************************


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