you don't have to use PyRx at all; and no need of mailing either; you can just use a simple shell script to run AD4 multiple times; However I recommend using AD Vina!

http://link.springer.com/article/10.1007%2Fs10822-010-9352-6

http://pyrx.sourceforge.net/faq

FAQ:4

What's causing "Open dlg file for details" error message?

When there are no docked conformation in the docking log file, PyRx shows the following error message.

Open output.dlg for details.

Docking instance has no attribute 'ligMol'

Docking instance has no attribute 'ligMol - is the error message that dlg parser throws. "Open "+outputFile+" for details" - is the message PyRx prints when it catches this exception. To troubleshoot this problem you need to open your dlg file and read it carefully to see why there were no docked conformation recorded there.

Dear Ratih,

Why are you using Autodock via PyRx. if you want to do multiple docking then you can write mail to me at [email protected] i will help you out in doing that

you don't have to use PyRx at all; and no need of mailing either; you can just use a simple shell script to run AD4 multiple times; However I recommend using AD Vina!

I recommend AutuDock Vina too, the scripting for multiple docking is more easier than autodock, and this version is parallelized so very faster than autodock.

furthermore, thereare some python programs as chimera whose purpose some very interesting graphical interface for vina, making conf files and visualized result as pdbqt.

Autodock vina is one of the best reccomended docking program which has a flexible algoritm

Dear,

Ratih

it could also be related to an incomplete Dlg file (i.e. the docking didn't finished or it wasn't successful), so the script is not able to find the docked coordinates to be summarized.

try to use autodock on a server maybe yo will get the docking result.

and you can consider "autodock vina" in pyrx. the wizard is so helpful.

good luck

you can try to use another autodock plug-in. get a look at: http://www.fc.up.pt/pessoas/nscerque/vsLab/vLab/HomePage.html

Thank you for your respond...very helpfull

Hello Ratih and other people.

I know this is and old thread, but I was facing the same problem and found it with no answer, and since I achieved solving it I'm posting it here in case somebody else needs it in the future.

Some of the ligands in my list were proceced and others not. So I tried starting all over again and making sure I was doing the same thing with all of them. The problem persisted, and the error was autodock being unable to find the files, even when they where there. I noticed that proceced files had shorter names than the causing error ones. So I proceed to shorten the name in all files to maximum 5 characthers and so the program was able to precess all of them.

So, if you are facing this trouble, just make the ligand file names shorter and everything must be ok.

Hope it's usefull for somebody in the future.