My AutoDock crashed when I clicked "choose torsion in currently selected residues", what's wrong with that?

Hello -

I am new to using docking software and I am trying to use Autodock Tools on my Mac (13.2.1). I open it from Terminal using the following command:

> alias adt='/Users/Shared/MGLTools/1.5.7/bin/adt'

> adt

The program opens but crashes when I try to Read Molecule. It worked once but now I am not sure what is happening. I have tried several different pdb files. Any advice would be great!

Hi, I'm trying to dock thousands of compounds using autodock vina. I already have the script for running the compounds without manually docking them one by one on the GUI of autodock tools.

However, I have thousands of ligands that I need to prepare and this is very time-consuming. Can someone help me with how I can prepare all the ligands all at once in a single batch? What I am currently doing is using the autodock tools GUI, then clicking Ligand > open > file > save as pdbqt. With the Ligand option in autodock tools, it sets the gasteiger charges, merges the nonpolar hy drogens and sets the TORSDOF. Is there a script which I can use so that I can perform the same without the need to manually use the GUI for each compound? thank you!

I conducted a 100ns simulation of my docked complex, obtaining a maximum RMSD of 4.2 Angstroms and an average of 3.1 Angstroms. Can someone help me how can I justify this high RMSD? I have attached a snap of the graph below.

As far as I have interpreted this graph. Initially, this is a gradual increase in RMSD but then it became stable with an average RMSD of 3.1. So basically this RMSD is high but is stable. But Why its value is high? Is it ok to have a high RMSD?

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.

What is the grid spacing that autodock vina used 0.375 or 1 angstrom? Some of the cases many have told that autodock vina used spacing 0f 1 angstrom but in some cases it is written as 0.375. So I am very confused. Please can anyone clarify this doubt?

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..

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?

Create flexible residues in Autodocktools