Autodock Vina Extended problem

[Sherif 0]

how can I score the bound ligand?

[DmitriyMarin]

In the docking parameters of the AutoDock Vina Extended, select "Score only".

[Sherif 0]

will there be any updates for this extension ? because it is very useful but it can get better

[DmitriyMarin]

Yes, there will be updates. What would you like to be added or modified in this extension?

[Sherif 0]

well, for me, In original AD Vina, you can prepare both receptor and ligand in the software. For me now, I have to use software such as chimera to minimize the protien, add charges, hydrogens. Same for ligands. If you add this to the extension, it will be good i think.

[DmitriyMarin]

Thank you for your feedback, @Sherif-0 !

You can prepare both receptor and ligand in SAMSON as well: add hydrogens e.g. based on residue types (for neutral pH for now, but we plan on extending this functionality), minimize using the built-in Minimizer (you can minimize a ligand and a receptor in separate documents, and you can apply the option of ligand minimization before docking in AutoDock Vina Extended). As for charges, they can either be provided in the input file or set using the Edit charges editor (Edit menu > Edit charges) or directly in the Inspector for selected atoms.

What are other missing functionalities that you would like to be added? We will try to add them.

[Sherif 0]

thats great. But I can not find the minimizer

[Sherif 0]

thank you i find it...

if i think of sth,i will tell you...

May be try to add different algorithms like genetic and lamarikan

[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