I think you are looking for protein-ligand conformation after docking has been performed right? You can use Chimera to create one pdb file i.e all of the docked posed in your protein could be seen in Chimera, or you can also use AutoDock GUI, it also provides you with the option to do so plus in autodock GUI the residue interactions in the active site can also be seen. Discovery studio visualizer is also an option.

You can use the clustering option in Autodock, where you rank the binding sites using histograms by energy. Then you click the histogram and the "average" of the conformations with that energy range will show, you should be able to save that as a pdb. Only one macromolecule and ligand should show on the output.

http://autodock.scripps.edu/faqs-help/faq/how-do-i-evaluate-autodock-s-clustering-results

or check this thread

https://www.researchgate.net/post/How_to_write_the_best_conformation_low_energy_complex_from_the_largest_cluster_using_script_python_from_the_dlg_file_while_running_AutoDock2

Hi Danish Jasnaik,

Thank you but I'm not familiar with Chimera because I'm using PyMol. Do you know how to generate one pdb file of a complex protein-ligand using pymol? For AutoDock GUI, I have been using it to view the ligand conformation and interactions with amino acid but I do not see option that we could build a complex of protein-ligand in one single file. Do you know how to do it?

Hi Walter Gonzalez,

Thank you. But that is for analyzing Autodock result. We won't be able to see cluster if we are analyzing Vina result in Autodock Tools. I know how to build protein-ligand complex for Autodock4.2 but I don't see the option for Vina. 

Hi Abdul Manas 

http://vina.scripps.edu/tutorial.html

I think this videos would help you. If not then let me know ill tell you how to do it using chimera.

Dear Danish,

I already watched the video and it doesn't tell us how to build a complex. Btw, it is already solved now. Thanks anyway!

Dear Abdul Manas,

I used vina_split program to split the multi conformation docking output *.pdbqt file, then wrote a simple Linux bash shell scipt to build the complex pdb file. Writing simple shell scripts you can make your molecular modelling more effective!

Try this-

Put your xxx.pdbqt output and protein.pdbqt in one folder.

Run the cygwin and go to this folder and follow only two command as -

1.       cut -c-66 xxx.pdbqt > xxx.pdb

(this creates pdb file from your output pdbqt. Edit this pdb so as to include only required conformer. e.g. if you want 1st conformer only keep model 1 in pdb and delete other models. Thus your pdb is having only one desired conformer now)

2.       cat protein.pdbqt xxx.pdb | grep -v '^END ' | grep -v '^END$' > yourname.pdb

(This creates the complex pdb of protein and xxx)

Good luck to analyse the complex...

Post your any related query and I would be happy to give suggestions. 

Dear Balazs and Rajesh,

Thank you very much! You guys really help!

Please use vina_split to split your file. now you have each conformation in complex with receptor. Then use mgltools or openbables to convert complex with pdbqt format to a file with pdb format.

Use following comends:

1) cd (go to directory)

2) vina_split.exe --input file address

Hi

I want to share my personal experience. There are several ways for combining ligand and receptor after docking. It can be done simply by using Open-BABEL. After docking was performed and .pdbqt files were generated one is able to select both ligand.pdbqt and receptor.pdbqt files simultaneously and convert them into one complex.pdb file with preserve coordinates. If one use PaDEL-ADV for screening all different pose of the ligand will be combined with receptor, then the preferred pose can be chosed in complex with receptor by using Chimera. The the complex file can be visualized by any software like Chimera and etc.... It also also can be used for MDS.

I agree with all here.

i m facing problem in converting docked file into .pdb format. autodock vina save ligand.pdbqt and receptor.pdbqt different and it do not save both molecule in .pdb format single file

plz help me m stuck

using autodocktools open the docking results file. then using the docking results and select the suitable docking position.then save it as pdb file.

open pymol. the open the protein pdb using pymol. then open the above saved pdb. then you can export the structure together in a single pdb

Try to following steps

1-first collect the highest docked score structure based on Autodock score in pdbqt format from docked file

2 convert it pdbqt to pdb using babel command eg:

babel -i pdbqt file.pdbqt -o pdb file.pdb -h

same thing convert protein/receptor using above babel command

babel -i pdbqt file.pdbqt -o pdb file.pdb (remove -h)

3 use this command

cat receptor.pdb my_docking.pdb | grep -v '^END ' | grep -v '^END$' > docked_complex.pdb

Thankyou all