AutoDock Tutorial Part 3- Prepare Macro molecule/Protein for Docking

[@ashinvel1625]

Thanku. Great help.

[@antonellafinali6315]

Hello! I have a question : is there a difference in using pymol for docking ?

[@sanjaisrao484]

Thanks

[@mahmoudel-nouby7402]

thank you for your efforts I have a question what about if the macromolecule is not a protein, I mean polymer for example

[@Cutebabydomain]

Why do we need. To assign AD4 type? My software is not showing this option in edit -atoms

[@ankita5258]

How to fix it if there are charges on residue you dont explain this because in my protein i found it now how to fix it

[@abrahamshinemathews8635]

Ore pwoli 👍👍

[@memunasaqib3801]

hello i have a question when i try to add hydrogen it is saying this protein have non bonded atoms how to delete them and how to further deal with the situation ? please guide

[@arafasaidali1760]

Sir how do i delete the hetero atoms and other chains of protein

[@covalentdrugsgroup1606]

Hi Aby Jimson, that's a great tutorial on AutoDock. I have installed 4.2.6, and while trying to set the atom type to AD4, I did not find this option in 4.2.6 version, and the protein is not being saved to PDBQT in the next step. Can you help with this issue?? Thanks.

[@TheAbzaby]

Which is your python version? make sure you have installed MGL tools. Also copy paste the required documents to workspace folder and try again

[@kakalisarkar6757]

Thank you so much. It was really helpful. I just have a single query. After preparing a protein in ADT, do we again need to go for energy minimization of this prepared protein so as to perform docking or we can simply carry out docking with this prepared protein exported from ADT?

[@TheAbzaby]

No. You may just proceed with the protein. Other softwares are needed if you are using some proteins which are difficult for AutoDock to handle.

[@kakalisarkar6757]

@@TheAbzaby Okay. Thank you!

[@TheAbzaby]

@@rasikaradhakrishnan6117 yes. We have already done it using autodock.

[@TheAbzaby]

@@rasikaradhakrishnan6117 For protein the autodock algorithms work fine. Various steps to correct the structure is sufficient. For ligand if we drew it or download then we may use various software like avogadro to do energy minimisation. But the above step is not that common for protein.

[@TheAbzaby]

@@rasikaradhakrishnan6117 i have not downloaded the ligand structure from PDB yet. I usually use pubchem or draw it. So avogadro is needed.

[@karreddularaja3756]

Is it similar for DNA instead of Protein

[@shabnama4523]

Sir, what if we have several subunits? In case of blind docking should we delete the other subunits or continue with the whole protein

[@TheAbzaby]

Dock with a single sub unit at a time. Or else the programme may crash. You may dock different subunits individually.

[@drawpryx]

why we have to delete heteroatom and add polar hydrogens, and what is AD4 type, what happen if I have been saved file as pdbqt without assigned AD4 type process. can you explant for me please

[@TheAbzaby]

Polar hydrogen are the ones which are attached to polar atoms. They must be added to calculate charges effectively. A more precise practice is to add all hydrogens, compute Gasteiger charges and then merge the non-polar hydrogen.

[@TheAbzaby]

Hetero atoms usually posses no significant role in docking and their parameters may not be added in AutoDock force field. so if you proceed without removing them you may get an error.So we delete them since mostly they are not part of the chain but just co factors

[@TheAbzaby]

It is important to assign the correct atom type in Autodock. The pdbqt file itself has q for charge and t for type. For most atoms, the AD4 atom type is the same as its element; the exceptions are "OA", "NA", "SA" for hydrogen-bond acceptor O, N and S atoms; "HD" for hydrogen-bond donor H atoms; "N" for non-hydrogen bonding nitrogens; and "A" for carbons in aromatic rings. The AD4 atom types and their parameters can be found in the "AD4_parameters.dat" file, which is included in the source code of the AutoDock 4 distribution

[@drawpryx]

@@TheAbzaby Thank you very much, I'll follow you method and comeback for more questions.

[@amy1996judith]

🤩🤩🤩🤩🤩🤩

[@corinbior9768]

Hi ,when i add kolman charge and then click on check total on residues appear to me alot of atom ,what i do ? Can i click on spread charge on over all atom?

[@TheAbzaby]

It may happen. You may select all residues and split charge deficit. But make sure that you have enough computing power to do so because it may be a tedious work.

[@corinbior9768]

@@TheAbzaby thank you ser,but should make box in exactly place of interaction between ligand and protien but how i make this if i not know what exactly place of interaction ,in case of aldose reductase and glucose interaction can you make docking and share it in youtube?

[@TheAbzaby]

@@corinbior9768 you should do a blind docking first. For this prepare a grid which includes the entire molecule and perform docking. Then identify the sites at which interactions takes place. Now repeat with a smaller box which accommodate only the intercation sites and some nearby residues.

[@ankitchatterjee3074]

@@TheAbzaby Sir, I was having 2 residues with non-integral charges and tried split charge deficit over all atoms of residue and it was showing some error... what to do?