Hi Mahmudunnabi

-read the molecule;

-Edit->Add Hydrogens [don't change the default values]

-Grid->Macromolecule...-> Choose

it will give you a saving option

Are you following the same steps?

Kollman charges adding are a part of a protocol so as far as i know need not worry about it.

The steps are as follows;

First, add hydrogen molecules, add kollmann charges, assign autodock4 and then save as .pdbqt. When saving as .pdbqt, remove the hetatoms alone. Your molecule is ready. Dont get panic, the protocol is default. Regards. Sridhar

Hi,

Danish

ya. i have followed the same procedure you mentioned  above. thank you.

Thanks Mr. Sridhar Sundaram