PyRx problem when using flexible residues

[silvergirl]

When I select flexible residues in the receptor (using the right-click method) and then I try to run Autodock, I get the following error message:


17:16:12: Error running C:\AUTODOCK\autogrid4.exe -p protein.gpf -l protein.glg
17:16:12: Working Directory: C:\Users\User\.mgltools\PyRx\Macromolecules\protein_flex
17:16:12: Stderr:

Can some one help me? Thank u!

[sargis]

Thanks for the message. You'll need to run this form a command line to troubleshoot it. First, are you able to run C:\AUTODOCK\autogrid4.exe without flexible residues?

[silvergirl]

Thank u for the rapid answer.
Actually, Autodock4 does not work either way. Only Vina works perfectly.
Can u help me with a possible solution to this problem? I'm running PyRx on Windows 7.

[sargis]

Thank u for the rapid answer.
Actually, Autodock4 does not work either way. Only Vina works perfectly.
Can u help me with a possible solution to this problem? I'm running PyRx on Windows 7.

U are welcome. This probably mean that AutoDock 4 isn't properly setup. We plan to include AutoDock 4 in the future PyRx releases, but for now you can trace-back the steps you did to put autogrid4.exe under C:\AUTODOCK to see what can be done to fix this. Do you get any error messages when you run C:\AUTODOCK\autogrid4.exe either by double-clicking on it or running it from a command line?

Thank you for using PyRx!

[silvergirl]

Hello again,

There was an error when I double-clicked the autogrid4.exe file. So I reinstalled and now it is working perfectly. Thank u for your help. If you don't mind, I'd like to ask another question. When I reach the "Analyse results" section, do I have to save the ligands one by one (by right-click>save as pdb)? Is there any way of saving all the ligands automatically? And saving the several conformations of one single ligand?
Thank u once more.

[sargis]

There was an error when I double-clicked the autogrid4.exe file. So I reinstalled and now it is working perfectly. Thank u for your help. If you don't mind, I'd like to ask another question. When I reach the "Analyse results" section, do I have to save the ligands one by one (by right-click>save as pdb)? Is there any way of saving all the ligands automatically? And saving the several conformations of one single ligand?
Thank u once more.

I'm glad you have autogrid4.exe working perfectly. When you reach "Analyse results" section, click on Edit -> Preferences menu, then Open Babel -> AutoDock Ligand -> "When Exporting SDF in Analyze Results" and change "Number of Poses to Retain" from 1 to 0.

pyrx_forum_pref.png (40.14 KiB) Viewed 1250 times

Now click on the Save as SDF icon located on the right part of Analyze Results toolbar

database_save.png (755 Bytes) Viewed 1250 times

This would save all the poses in SDF file that you can use. Remember that you can also write your own script to do further analyses. You own all the results and they are located underC:\Users\<USERNAME>\.mgltools\PyRx

Thank you for using PyRx!