Possible bug parsing PDBQT file

Scoring and Minimization with AutoDock Vina

Status: Beta

Brought to you by: dkoes

Possible bug parsing PDBQT file

Forum: Help and Feedback

Created: 2016-05-04

Updated: 2016-05-22

Miro - 2016-05-04

When I run smima on certain pdbqt files:

smina --receptor 4w9n_protein.pdbqt --ligand 4w9n_ligand.pdbqt --flexdist_ligand 4w9n_ligand.pdbqt --out 4w9n_ligand_min.pdbqt --out_flex 4w9n_flex.pdbqt --log 4w9n_ligand_min.log --flexdist 5 --minimize

I get the following message:

Parse error on line 5 in file "4w9n_protein.pdbqt": ATOM syntax incorrect: "7 37.29" is not a valid coordinate

However, the input files are identical to others (attachments in reply):

ATOM 1 N HIS D1530 13.177 31.357 37.290 1.00 0.00 0.615 N

Except maybe in the fact that the residue number contains 4 digits and therefore there is no space between it and the chain ID.

Last edit: Miro 2016-05-04

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Miro - 2016-05-04

Attached the input files.

4w9n_ligand.pdbqt

4w9n_protein.pdbqt

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David Koes - 2016-05-04

I can't reproduce this. Are you running a recent version? I tried with the binary available from Sourgeforge and didn't have problems:
Smina Apr 2 2016. Based on AutoDock Vina 1.1.2.

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Miro - 2016-05-04

No, I compiled it from source (git) last week. I will try the precompiled version.

Last edit: Miro 2016-05-04

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David Koes - 2016-05-04

Just rebuilt the current source code and couldn't reproduce with that binary either. I suppose it is possible that the issue is your openbabel version.

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- Miro - 2016-05-04
  
  Hmm. It is the stable release 2.3.2 installed via the package manager in Ubuntu 14.04... Which one are you using?
  
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David Koes - 2016-05-04

I build from the master branch... did the smina.static binary work?

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- Miro - 2016-05-04
  
  Yes, it does. So you are using the OpenBabel development version 2.3.90, right?
  
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David Koes - 2016-05-04

Correct.

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- Miro - 2016-05-04
  
  Confirmed. Compiling with the OB development version solves the issue.
  
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  - ZhenyOK - 2016-05-22
    
    Where have you got it? Unfortunately I was not able to find anything newer than 2.3.2 =(
    
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David Koes - 2016-05-22

https://github.com/dkoes/openbabel

Will give you exactly what I use.

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- ZhenyOK - 2016-05-22
  
  Thanks a lot!
  
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