What are Gasteiger charges and Kollman charges in the context of molecular docking?Why is it important to add them during protein preparation?

I am trying to do a docking between a ssDNA aptamer with an organic molecule using Autodock4. I have reviewed papers where they add Gasteiger charges to the aptamer but they don't mention anything about the organic molecule.

In Autodock4, after adding Gasteiger charges also to the ligand I get an "error" that does not allow me to save the *.pdbqt file of the ligand.

Is it necessary to add payloads to this ligand in Autodock4? I did this same procedure in AutodockVina and I had no problems there.

hi, how can I calculate RMSD using Pymol? (tutorial)

How can I calculate the RMSD  value between crystal and docked structure of ligand using pyrx or VMD? Is it possible to calculate RMSD using pymol between the two ligands (crystal and docked)?

Need a download link

Can anyone help me to understand about exhaustiveness and energy range in auto dock vina and also help me to understand the default value of exhaustiveness=8 and energy range=4?

Thanks..

Hello everyone,

I am trying to do molecular docking using AutoDock Software. One of the struggling I am trying to deal with is generating Grid Box. How can I generate Grid Box without knowing active binding sites of the protein? Should I keep the Grid Box positions as default, or should I change it according to the binding site? Sorry for the inconvenience.

Thanks in advance,

Mervenur

I used AutoDock Vina to make docking of some small organic compounds on a protein. I did this using the interface of UCSF Chimera, and it allowed me to use an exhaustiveness of 8 (the maximum default value). I tried the same docking, with AutoDock Vina but this time from the AutoDock Tools interface. Since this time the order came from a Config file that can be edited, I changed the exhaustiveness value to a higher one (80) to see if the results were the same. As the results came, I noticed minimal changes from the poses generated with 8 or 80 exhaustiveness. How high can I change the exhaustiveness value to get better poses? Or there is a limit for the exhaustiveness when no further improvement can be obtained?

i am docking ligand against urease enzyme PDB:ID 3la4. active pocket contains Ni atoms. but during process software gives error of adding parameters of Ni first.

how to add these parameters and save file?

Why I am getting a lot of models of the same docking study?How will I know which one to choose?