Flexible Side Chains in Pyrx/Vina Wizard

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Flexible Side Chains in Pyrx/Vina Wizard

Postby kchemistry » Tue Jun 04, 2013 6:26 pm

Hello,

I am an undergraduate using Pyrx and the Vina Wizard to screen a 1.500 compound library for ligands that may inhibit the protein that my lab studies. I know that with autodock vina it is possible to have flexible side chains in the protein search space. Does anyone know if I can manipulate this setting using the Pyrx GUI?
I have been searching online for sometime now, and I cannot seem to find this information.

Thank you in advance for your time,

Kristen
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby sargis » Tue Jun 04, 2013 10:57 pm

Hello Kristen,

To make flexible side chains, load your molecule in PyRx, then select residue(s) under Navigator -> Molecules, right-clicking on them and use AutoDock -> Flexible Residues. This creates _flex folder under Navigator -> AutoDock -> Macromolecules as shown in the image below.
Image
When using Vina Wizard, you just need to select this _flex folder and PyRx would run Vina with flexible side chains.

Hope this helps and thank you for using PyRx!
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby kchemistry » Thu Jun 06, 2013 7:04 pm

Thank you for your help. Everything went smoothly, until the very end. After Vina ran, it did not display any poses and binding affinities in the analyze results tab, so I have no csv or sdf files to save. I don't know if this is related, but I also noticed the 'time watch symbol' flickering in and out when I move my cursor anywhere in the 3D scene tab. Do you have any idea what may be causing this?

-Kristen
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby sargis » Thu Jun 06, 2013 8:56 pm

You are very welcome Kristen. Something must have gone wrong after Vina ran. Did it create Vina output files. Also, what OS and PyRx version are you using?
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby kchemistry » Fri Jun 07, 2013 2:56 pm

Hi Sargis,

I'm not sure what version of Pyrx I am using, I can't seem to find a name for the file other than pyrx.app, although I'm pretty sure it's version 0.8. I downloaded it from sourceforge last summer. My OS is Mac OS X 10.6.8, and there are two output files in the pyrx output folder. One for my protein - flex version, and one for my ligand (I'm just using one ligand at the moment). However, as I mentioned, there is nothing under the 'results' tab and thus no output csv or sdf files for me to save.
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby sargis » Sat Jun 08, 2013 4:37 pm

Hi Kristen,

Thanks for the info. Unfortunately I won't be able to provide any fixes, unless I'm paid for that. Please try 0.9 version on Linux, if possible. This problem might be specific to Mac OS X, or perhaps it has been already fixed in 0.9 version.
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby kchemistry » Mon Jun 10, 2013 6:09 pm

Ok, thank you.

You've mentioned the compensation issue on this forum before. Do you have a paypal donation account, or any way for users to pay you for your time and help?
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Re: Flexible Side Chains in Pyrx/Vina Wizard

Postby sargis » Tue Jun 11, 2013 12:54 am

You are very welcome. Please visit http://pyrx.sourceforge.net and click on Support This Project on top left.

Please attach rigid, flex, and ligand pdbqt files to this post or email them to me at dallakyans @ gmail.com. Of course, you get your money back if I'm not able to help you.

Thank you!
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