Autodock Vina Extended problem

DmitriyMarin

Home menu > Minimize

Click on it and it will start minimization of all molecules in the document using the Universal Force Field. To stop the minimization click the second time. You can see the minimization data in the top-left corner of the Viewport.

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