ADL: Charges for AutoDock Vina

Gianluca Interlandi gianluca at u.washington.edu
Wed Oct 7 11:02:01 PDT 2020


Thanks Ming! In case someone uses AutoDock4 instead of Vina, I found in 
the AutoDock FAQ that "the AD4 scoring function was calibrated using 
Gasteiger partial charges on both the ligand and the macromolecule":

http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Scientific%20Questions

However, in another tutorial it recommends that one should use Kollman 
charges for the macromolecule (Gasteiger for the ligand):

http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-with-autodocktools/UsingAutoDockWithADT_v2e.pdf

Not relavant to me right now as I'm using AutoDock Vina. Maybe for the 
future.

Best regards,

            Gianluca

On Wed, 7 Oct 2020, Ming Hao 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 ---
>
>

-----------------------------------------------------
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.
-----------------------------------------------------




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