I don't think you should remove original ligand structure while performing the redocking. For RMSD calculation, u can check your .DLJ file

Since Autodock Vina does not give you RMSD value with respect to a reference conformation (like Autodock 4), you can calculate it using Autodock Tools (v. 1.5.7). To do so, open both the original and redocked conformations into Autodock Tools, right click on one of them in the control panel, then click on RMSD/Superimpose.

You've answered to your question, so what is the problem? You want to compare the docked and the co-crystallized ligand positions.

thank you for your answers. However I can not find the RMSD/superimpose command in adt!

Are you using adt version 1.5.7 or higher? I guess this command is just available for those newer versions

I'm attaching to this comment two pictures to show you how to do it. Hope it helps

Oh that's why! I have adt 1.5.6.

Thanks!!!

last question: what if the two ligands have not compatible atoms labels?

How did you perform your redocking? I have not faced this label problem yet but you could re-label atoms manually according to the reference structure.

Also, you can test Discovery Studio (it is free for academics) for calculating rmsd in redocking experiments.

For my re-docking I have removed the original ligand and water molecules from the protein crystal structure.

Then, I have minimized the energy of the ligand (with chemdraw and its MM2 command for energy minimization) and I have added polar hydrogens and charges in the protein structure (with vina).

Finally, I have performed the docking with autodock vina.

The result is really close to the original position of the ligand; I have manually calculated the RMSD (the ligands are quite small and it does not take a long time, considering that hydrogens are not included in the rmsd calculation).

I have measured the distances between each pair of atoms using pymol (see figure below) and applied the formula reported in this paper :

Article Methods of Protein Structure Comparison

that is the formula to calculate the root-mean-square deviation.

Hope this makes sense!

Thanks again for your help!

Dear Vitor Rabelo Sir,

How you opened two ligand in Autodock. I think one is *.dlg and another one is *.pdbqt. Am i right. I was opened these two file format but i didn't find RMSD/superimpose. Vitor Rabelo

Krishna Kumar Varshney

You're right! You can open the docking result as dlg and the reference structure either as pdb or pdbqt (file > read molecule). As mentioned before, the RMSD calculate option is only available for ADT 1.5.7, not for older versions. You can check the pics that I sent in previous comments to check where you can find this option in the side bar of ADT 1.5.7.

@Vitor Rabelo sir,

I was tried but truly I'm unable to do! So please make a little video after this process analyse>docking>open>*.dlg, plz do me this favour. Plz send me that video clip on [email protected]

Thanking you for this kind of helpness

i attached a file. i found 0.000 rmsd value. 2 ligands are not open simultaneously, even one file is *.dlg and another one is *.pdbqt

Krishna Kumar Varshney

I can see only one conformation in your fig. I guess you should select one conformation from your dlg file before calculating RMSD using this option. When you open your dlg, the first pose is the same as you used as input for your docking (maybe your reference structure?). Thats why i think you are finding a RMSD value of zero.

Are you using Autodock 4.2.6 or Vina? If you are using Autodock 4 (which if think so because you have a dlg file), there is no point for calculating RMSD like this. First, open your dlg file using the using the "Analyze" tab in ADT. Once you have chosen the conformation to check, click on "&" button, then check the "Show info" option (take a look at the attached figure). In this window, you can find information, including the reference RMSD (refRMSD) between the conformation you are analyzing and the initial one (the one submitted for docking purposes). If you are not using the crystal structure as the initial conformation, then you have to use the "RMSD/superimpose" option as explained previously.

Thanking you for such kind of suggestions Sir!

One more query I have, How to perform redocking/overlay using adt 4.2? I'm user of mgl 1.5.7 rc1, where we call also find out rmsd value easily.

ADT is a graphical user interface for autodock. You probably use both autodock 4 and autogrid4 to run your docking.

Yes, I did install autodock4 and autogrid4 in mgl tool 1.5.7. Now, how will i perform redocking/overlay as i attached picture which i downloaded published paper.

You may go through this blog

https://dlcompbiotech.blogspot.com/2021/05/calculation-of-rmsd-values-between-two.html