Hi,

I think it doesn't matter if you used PyRx or ADT because they are just an interface to facilitate virtual screening and docking analysis, respectively. What program did you use to perform the docking? autodock 4 (ad4) or vina? You should know what type of output are you getting from the docking protocol. For example, the dlg and pdbqt files are the output for ad4 and vina, respectively. Remember that you can edit a pdb file by using a text editor. So, you could open your pdb as text file, copy and paste all the information of the receptor in new file. Then, using the same text editor you can manually extract the coordinates of the best pose of your docking results and paste together after of the last line of your new file that corresponds to the coordinates of your receptor. You should be able to inspect your complex file by using a molecular visualization program (e.g. Pymol, Chimera, etc).

Best,

Aldo

You can use autodock tools

Aldo Segura-Cabrera, you are the man dude....

you are just right.... I got clicked... and found the way out....

Here is what and it gonna work....

As you said to "manually extract the coordinates of the best pose". you don't have to do it manually. There is an option to save the resultant poses in sdf format in pyrx. So what if we use it to save the best pose initially in sdf format. then use open babel to change the format to pdb and then proceed to manually edit the receptor coordinate file by adding coordinates of converted pose at the end. Thats it... It worked... thats aawsome.. Thank you ...

Dear Rohan Meshram

you can use MGL tools where you will be able to get the pose of all the iteration along with interaction values. Its good with ADT 4.2 in PyRx in combination with MGL tools for visualization, but even though you can run VINA with PyRx, but can not get the poses out of MGL tools.

Also Aldo Segura-Cabrera and Manish j Patel, I would like to discuss which would be the best to visualise and get energy values of inhibition constant, binding energy and details of hydrogen bond interaction with VINA. If I read the .dlg file generated by VINA in MGL tools, I get an error. Kindly provide me some suggestions and ideas.

I think VINA won't calculate inhibition constant, hydrogen bonding etc. because of this Vina is faster than Autodock4.2. But i prefer to use Autodock4.2 if you have even 100 molecules for docking than vina. Autodock4.2 wont take much time also and will give detailed information about IC, hydrogen bonding, binding energy etc so that at the end you have clear idea how exactly each compound is interacting. WIth Vina you may miss compounds having potency to act as lead molecules.

Yes dear Prashanth, but Few article reviewers these days reply a comment saying that older version of AutoDock has been used, that is ADT vina could be used instead of ADT4.2 and they also have a reference on the webpage of Vina saying that it is much more accurate than ADT4.2. Then how about this ? I just have one thing to say ADT Vina also generates .dlg files ultimately, and in MGL tools we also have an option saying 'analyzing Vina results', but we get an error when we try to call the vina result file. I just want to know what this is. I have even discussed in Scripps research institute blog, but I didn't get any workable reply. How to solve this contradictory matter???

If your data is published, could you please send any vina dlg file and also protein *.pdbqt file. I will have a look and think of possible solutions.

Data wasn't published and the article was from EJMC rejected due to some controversies even in the synthesis part of my collaborator. So he is planning for some other journal.