smina / Discussion / Help and Feedback: parse error

parse error

Forum: Help and Feedback

Creator: Thomas Vargo

Created: 2022-05-12

Updated: 2022-05-17

Thomas Vargo - 2022-05-12

get this error:
'Parse error on line 4 in file "1OYT-FSN.pdbqt": Unknown or inappropriate tag'
with this command:

smina -r 1OYT-receptor.pdbqt -l 1OYT-FSN.pdbqt --autobox_ligand 1OYT-FSN.pdbqt --autobox_add 8 --exhaustiveness 16 -o 1OYT-redock.pdbqt

pdbqt files were generated from pdb files with openbabel 3.1.1 using:

obabel 1OYT-receptor.pdb -xr -O 1OYT-receptor.pdbqt obabel 1OYT-FSN.pdb -xr -O 1OYT-FSN.pdbqt

I'm new to command line work in general, and have a new macbook pro M1.
After reading the other help discussions I think I could have an issue with my openbabel versions, but i'm not sure how to fix that.
in my terminal in 'base' or my env i get:

obabel -V

Open Babel 3.1.0 -- Oct 27 2021 -- 21:57:10

installed using:

brew install open-babel

Thanks in advance from a Pitt Chemistry Alum!

Tom

1OYT-FSN.pdb

1OYT-FSN.pdbqt

1OYT-receptor.pdb

1OYT-receptor.pdbqt
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Thomas Vargo - 2022-05-17
  
  Resolved:
  uninstalled and reinstalled everything!
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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