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PostPosted: Thu Jul 02, 2009 2:37 pm 
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Joined: Wed Jun 24, 2009 2:28 am
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I did rigid body docking using vina for two protein subunits are closer, results are not that useful to me, so
wants to do flexible docking by selecting few residues close where I do expect some binding.

I have two pdbqt files one with full model and another with only residues that I am interested. While running vina
I did get error message?
Prefix for flexible side chains will be flex.pdbqt
Detected 2 CPUs
Reading input ...

Parse error on line 1 in file flex.pdbqt: Unknown or inappropriate tag
Processing ligand 00131.nci_2

then it fails.

My question what are the procedures to do flexible docking? I do have to keep only side chains not the main chain?
How to define the residues in rigid and flexible residues?

Thanks for suggestions


PostPosted: Thu Jul 02, 2009 6:09 pm 
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Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
I just added an entry linking to the explanation on top of this forum.

If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.

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