Autodock Tutorial

[shalintripathi]

Really very Educative Video Thanks For Making Such remarkable Tutorial...:P

[chandramouliem]

@shalintripathi

Thank you very much dear Shalintripathi :)

[MultiAjao]

Hi,

The video is highly educative. you are appreciated.However,when I saved the result under write complex.Pymol or any other protein viewer did not see it and I could not upload it.What should I do??

[chandramouliem]

@MultiAjao :

Dear MultiAjao, pymol by default won't show the files with the extension .pdbqt

if you want to veiw it in pymol, then change the file type to *.*.* in pymol so that its visible

another suggestion is that open the complex PDBQT file in ADT and save it as PDB so you won't face any problems of visualization

[theFenianGurl]

Should the pdb protein files have their energy minimized? I have downloaded protein pdb files from the pdb and I have removed the ligands so as I can dock in ligands with alterations. I have used spartan to do this. I think the problem I am having is mainly due to the charges! I cannot add gasteiger charges to the protein! it says that the NA and about 12 O atoms have zero charges! how can I add charges to the protein? even in Spartan before the docking?...

[theFenianGurl]

Hey this video has been so helpful, thank you! but I cannot seem to get autogrid or autodock to run, when it does run it detects oxygen atoms that have a zero charge! how do I apply a charge to the oxygens in order for the autogrid to work! Im new to this software! Im also having problems with the gpf glg and dpf and dlg files! how do u save the log files? does it save automatically?

[chandramouliem]

@theFenianGurl : Hello Fenian, thank you for using my tutorial

which part of the docking doesn't contain charge on oxygen atoms whether ligand or receptor, can you please check if your ligand's structure has been properly optimised or not.(I refere gabedit an open source tool or sybyl/material studio the commercial tool to build the ligand model and optimise it properly using steepest descent or conjugate gradient methods of energy minimisation.

[theFenianGurl]

@chandramouliem Hello chandram,

I have built the ligan using spartan and I have minimized its energy conformation. I am using adt as you are here in this tutorial. I can save the gpf and dpf files no problem. But I cannot open them with autodock when i type the command into the terminal. Also how does one make the log parameter files? thank you so much for your help! :)

[chandramouliem]

@theFenianGurl .... continue.....

if the problem is there from protein, then please refine it using vmd or gromacs

[thanhmyvn]

Could you please tell me how to optimize the ligand. I use some software running on window, but finally I cannot save it as .pdb or .mol2 for Autodock. Thank you very much.

[thanhmyvn]

Could you please tell me how to optimize the ligand. I use some software running on window, but finally I cannot save it as .pdb or .mol2 for Autodock. Thank you very much.

[chandramouliem]

@thanhmyvn :

Hi there,

I am using linux and for drawing molecules I use Draw tool available in a software called Gabedit.

you can draw any molecule of your interest in that and you can save that as different formats like PDB, MOL2, MOL, XYZ etc., the molecule designed can optimized using newtonian methods or steepest descent or conjugate gradient to attain appropriate steric configuration.

have a nice day :)

by

Chandramouli )\/(

[thanhmyvn]

@chandramouliem

A big thanks to you! Have nice day :))

[oooorja]

Hi Chandramouli, This is a true tutorial for some of us students. I could follow it very well till the "Run Autogrid" step. I don't have 'Terminal window". I use windowsXP. So I used the Run AutoGrid under Run option. Unfortunately it rolled out all the set parameters and then said the process was unsuccessful as it could not find my protein.pdbqt file. I had made sure it is there in the folder. I went through the entire process carefully thrice and still same results. :( Can u please help? thx

[knkash]

There is message appear to me when I run the autodock,that it can not find or open the ligand..

any one know,how to solve it ?

[kaav06]

Hi, The tutorial is good. Very helpful but i am stucking at certain stages like before writing the dpf file. After i select docking->output->lamarckian GA its generating a warning saying that " you must chose macromolecule before chosing dpf" . Please clarify this. Thank you.

[srikrishnakarthik]

Hi, ur tutorial was really informative.. thanks alot.. This is helping me do my project..

but initially, u said there is something else called flexible docking, which we can learn after learning rigid docking. do you have a tutorial for that?

[gouthamikanduri]

hi...Thank you for your reply...I downloaded the autodock from autodock website,but I am unable to understand the algorithm (i.e need to do something at command line) and install it..is there any chance to post video of downloading and insatlling the autodock for mac (mine was mac 10.6).....is that possible 4 u? it will be very helpfull for me....

[gouthamikanduri]

Hi,please tell me how to download autodock in mac

[chandramouliem]

@gouthamikanduri : Dear Gouthami, you can download those binaries AUTODOCK: from scripps reserach institute and ADT, the GUI tool kit from MGLtools website, you can just google and get it, in this page links do not seem to be accepted paste the URL.

[wildentry76]

excellent videos a big thanks to you . i really understood the operation very well it was structured nicely and i appreciate your patience in typing and explaining keep it up

[chandramouliem]

@wildentry76 : Thank you very much...

[navjeet0211]

Hi.. Mouli... good work

It will be better if u rename it to Autodock tutorial by this more people will get to know about it....

[chandramouliem]

@navjeet0211 : Thank you for your advise navjeet, I changed the name to make it more specific.

[chandramouliem]

@Mahesh: Thank you dude

[maheshuohyd83]

Hi,Mouli its very useful for starters keep rocking