Body: <p>I am trying to dock ligands with proteins to estimate the docking potential however, I am facing this error while docking. Any help will be highly appreciated.</p>
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Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-13T23:37:27.240Z
Comments.Text: could you share the content of the line 574 of the Spike_C.pdbqt file? You can use `sed` for select one line after and one before of the 574 specific line  `sed -n '573,575p' Spike_C.pdbqt`
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-14T08:47:25.457Z
Comments.Text: Could you also let us know how you converted your ligand to the PDBQT format (`prepare_ligand4.py`, obabel etc.)
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-14T08:47:36.660Z
Comments.Text: Also (minor point), having the grid box the size of your protein (270_000 Å) is not a good idea: you may know where the ligand binds —i.e. receptor binding domain. In the case of a VLS you _want_ scores for it to bind there. Otherwise a lot will stick to the energetically unhappy transmembrane domain doing nothing.
Comments.UserDisplayName: Matteo Ferla
Tags: <database>
Title: Parse Error while using AutoDock Vina
ThreadText: # Parse Error while using AutoDock Vina
  
  (Asked by: username_0 on 2020-08-13)
  
  I am trying to dock ligands with proteins to estimate the docking potential however, I am facing this error while docking. Any help will be highly appreciated.
  
  [![enter image description here](https://i.sstatic.net/Jm0mr.jpg)](https://i.sstatic.net/Jm0mr.jpg)
  
  **Tags:** database
  
  > **Comments:**
  > **username_1**: could you share the content of the line 574 of the Spike_C.pdbqt file? You can use `sed` for select one line after and one before of the 574 specific line  `sed -n '573,575p' Spike_C.pdbqt`  
  > **username_2**: Could you also let us know how you converted your ligand to the PDBQT format (`prepare_ligand4.py`, obabel etc.)  
  > **username_2**: Also (minor point), having the grid box the size of your protein (270_000 Å) is not a good idea: you may know where the ligand binds —i.e. receptor binding domain. In the case of a VLS you _want_ scores for it to bind there. Otherwise a lot will stick to the energetically unhappy transmembrane domain doing nothing.  
  
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  ## 0 answers
  
  