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 Post subject: Visualizing Vina results
PostPosted: Tue Jul 14, 2009 5:17 pm 
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Hi everybody,

I've been using AutoDock4 for sometime and very recently switched over to Vina. I followed the tutorial and noticed the following:

1. Creating an all.pdbqt line in conf.txt as suggested is problematic. Vina gives an error message ("Configuration file parse error: unknown option all")
2. Upon removing the <all> line, Vina generates an output (ligand_out.pdbqt) of 10 different conformations with decreasing energy

My question is, can PMV be used to visualise the conformations, identify Hbonds, etc without a .dlg file as in AutoDock?

Thanks in advance

George


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PostPosted: Thu Jul 16, 2009 11:13 pm 
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Quote:
1. Creating an all.pdbqt line in conf.txt as suggested is problematic. Vina gives an error message ("Configuration file parse error: unknown option all")
2. Upon removing the <all> line, Vina generates an output (ligand_out.pdbqt) of 10 different conformations with decreasing energy


This is explained on the tutorial page, above the video.

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PostPosted: Thu Jul 16, 2009 11:16 pm 
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gtzotzos wrote:

My question is, can PMV be used to visualise the conformations, identify Hbonds, etc without a .dlg file as in AutoDock?



I've been told this can be done for arbitrary molecules (not necessarily from *.dlg). Perhaps ask in MGLTools?

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PostPosted: Wed Jul 22, 2009 6:42 am 
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first of all thanks for noce video tutorial for vina..i was interested to know wherther there is any way to extract out the best pdb-ligand confermation :shock:


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PostPosted: Thu Jul 23, 2009 10:09 pm 
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Look into "vina_split"

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