ADL: Vina Run for Docking

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ADL: Vina Run for Docking

Refat Sharmin
Hi,

I am facing a problem while running vina for docking  with our Protein
model and DrugBank approved ZINC ligand.  Everytime I am getting
following error: " could not open protein_model3.pdbqt  for reading".

The protein structure was determined by using I-TTASSER and converted to
pdbqt format by using OpenBabel2.3.2a. The protein structure  (both pdb and
pdbqt format), lingand  and the config file are attached here.

Can anyone help me to fix this error.

Thanks

Urmi

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config.config (204 bytes) Download Attachment
protein_model3.pdbqt (76K) Download Attachment
protein_model3.pdb (54K) Download Attachment
catechin_119978.pdbqt (3K) Download Attachment
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Re: ADL: Vina Run for Docking

Ruth Huey
Hi,
It appears that protein_model3.pdbqt was formatted by openbabel as a flexible ligand pdbqt file with 254 rotatable bonds.

Use the '-r' option to create a rigid receptor pdbqt file:

Here is the documentation string from openbabel:

obabel -H pdbqt
 
  AutoDock PDQBT format
Reads and writes AutoDock PDBQT (Protein Data Bank, Partial Charge (Q), & Atom Type (T)) format
Note that the torsion tree is by default. Use the ``r`` write option
to prevent this.

Read Options, e.g. -ab
  b  Disable automatic bonding
  d  Input file is in dlg (AutoDock docking log) format

Write Options, e.g. -xr
  b  Enable automatic bonding
  r  Output as a rigid molecule (i.e. no branches or torsion tree)
  c  Combine separate molecular pieces of input into a single rigid molecule (requires "r" option or will have no effect)
  s  Output as a flexible residue
  p  Preserve atom indices from input file (default is to renumber atoms sequentially)


Specification at: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file

 Best wishes,
    Ruth

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Refat Sharmin [[hidden email]]
Sent: Monday, May 05, 2014 10:16 AM
To: [hidden email]
Subject: ADL:  Vina Run for Docking

Hi,

I am facing a problem while running vina for docking  with our Protein
model and DrugBank approved ZINC ligand.  Everytime I am getting
following error: " could not open protein_model3.pdbqt  for reading".

The protein structure was determined by using I-TTASSER and converted to
pdbqt format by using OpenBabel2.3.2a. The protein structure  (both pdb and
pdbqt format), lingand  and the config file are attached here.

Can anyone help me to fix this error.

Thanks

Urmi

________________________________________________
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