Autodock Vina Extended problem

[DmitriyMarin]

Please note that the minimization of a big protein might take some time. You can also use the Gromacs Wizard for protein minimization.

[Sherif 0]

thanks so much.. i am enjoyng this software

[DmitriyMarin]

Thank you, @Sherif-0 , for your feedback!

[Sherif 0]

Hi

i think you can add the parameters same as present in AD Vina.. like number of seed generations, the algorithm used , etc...

[DmitriyMarin]

@Sherif-0 ,

We will add the seed number in the next version. What do you mean by specifying the used algorithm?

[Sherif 0]

well i was mistaken i am sorry

[DmitriyMarin]

Thanks for the reply. No problem!

[Sherif 0]

why dont you add the possibility of adding kollman and gastegier charges like in autodock tools.
so we can add H, charges, minimize the protien in the same application

[DmitriyMarin]

Dear @Sherif-0 ,

Vina doesn't require and doesn't use assigned partial charges for atoms, quoting the Vina manual: "assigning atom charges is not needed", "AutoDock Vina ignores the user-supplied partial charges" (see http://vina.scripps.edu/manual.html). So there is no need in adding Kollman or Gasteiger charges.

[Sherif 0]

Thanks this is very good to know