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PostPosted: Thu Jul 23, 2009 4:55 pm 
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Dear Gurus,

In MGLtools and autodock 4 your docking results were viewable in a nice format such that you could use that & command to create a joint pdb file. This was very convenient for comparing RMSD between different structures and the original structure.

With Vina results, i haven't been able to fiure out how to make a single pdb file of the protein and inhibitor, or how to calculate the RMSD between the original x-ray structure and a vina docked structure.

Does anyone have any hints or tricks on how to do this?


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PostPosted: Thu Jul 23, 2009 9:59 pm 
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The output format is almost the same as the input format. (You can use "vina_split" to make it exactly the same)

By design, this is the format native to ADT, so you should be able to use ADT to convert the files to PDB or other formats, etc. I suggest asking in the MGLTools forum about what you can do in ADT/PMV.

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PostPosted: Thu Jul 23, 2009 10:12 pm 
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Can you explain a little bit better how vina_split works? How would I use it for what you are describing?

I didn't see it's functionality explained in the Manual.

I will ask over in the MGLtools about vina viewing.

Thanks for the quick reply!

Jonathan


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PostPosted: Thu Jul 23, 2009 10:13 pm 
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vina_split is a relatively new addition (v 1.0+)

Code:
vina_split --help


should be self-explanatory

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PostPosted: Thu Jul 23, 2009 10:48 pm 
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In advance, please forgive my naivete

oleg_trott wrote:
should be self-explanatory


My version gave me this:

Input:
--input arg input to split (PDBQT)

Output (optional) - defaults are chosen based on the input file name:
--ligand arg prefix for ligands
--flex arg prefix for side chains

Information (optional):
--help print this message
--version print program version

and I managed to create a nice mess of files all split up into little bits. Thank you!

That being said, however, I am not sure exactly how to control the output. BY that I can't seem to figure out what 'arg' or variables (or where to find them) are available for 'prefix for ligands' or for 'side chains'.

I would find a bit more explanation helpful.


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PostPosted: Thu Jul 23, 2009 11:37 pm 
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Quote:
BY that I can't seem to figure out what 'arg' or variables (or where to find them) are available for 'prefix for ligands' or for 'side chains'.


Those prefixes can be chosen by you. Try "foo" for one and "bar" for another.

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