<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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CC BY-SA 4.0
2020-08-13T23:37:27.240Z
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`
zorbax
CC BY-SA 4.0
2020-08-14T08:47:25.457Z
Could you also let us know how you converted your ligand to the PDBQT format (`prepare_ligand4.py`, obabel etc.)
Matteo Ferla
CC BY-SA 4.0
2020-08-14T08:47:36.660Z
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.
Matteo Ferla
<database>
Parse Error while using AutoDock Vina
# 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

