A little problem

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A little problem

Postby saharinku » Fri Apr 12, 2013 5:53 pm

Hi I have been using Pyrx for my docking project. But when I try to dock using the receptor molecule I am sending with my list of ligands its not running.May I request if you could try on your side . I am running 0.8 version in windows.

Best Regards
saharinku
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9-A9.pdbqt
Ligand2
(1.47 KiB) Downloaded 186 times
9-A2.pdbqt
Ligand1
(1004 Bytes) Downloaded 186 times
receptor1.rar
Receptor
(129.86 KiB) Downloaded 155 times
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saharinku
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Re: A little problem

Postby sargis » Fri Apr 12, 2013 6:43 pm

Hi saharinku,

Are you running AutoDock 4 or Vina? PyRx version 0.8 in windows doesn't include AutoDock 4 binaries, that's why only remote execution mode is enabled for AutoDock 4 unless you download and install AutoDock 4 binaries locally. Unfortunately, remote execution of AutoDock and Vina is no longer working since these web services are no longer available - pyrx.sourceforge.net/downloads/71-known-issues


Thank you for using PyRx!
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Re: A little problem

Postby saharinku » Fri Apr 12, 2013 7:31 pm

Hi Sargis
I have local installation of Vina that I want to use. It seems when I try loading this molecule into pyrx and try to use vina it crashes. But when I try a different receptor and ligand it works fine.
Thus wanted to ask if the receptor molecule I send is too big .It has only one chain .
Greatly apprceiate all suggestions.
Best Regards
Rinku
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Re: A little problem

Postby sargis » Fri Apr 12, 2013 9:21 pm

Hi Rinku,

Thanks for the info. I wasn't able to convert receptor1.pdb into pdbqt. Not sure about the cause of crash either. I'll update you if I have a chance to look into this.

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