search

protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
43 stars 15 forks source link

Invalid file format for file #38

Closed kexul closed 3 years ago

kexul commented 3 years ago

Hi, here is the code I used:

pro = Protein('6TOL', ligand_ref='201')

which raised an error:

parmed.exceptions.FormatNotFound: Could not identify file format
msuruzhon commented 3 years ago

Hi, it seems that this is due to a bad SDF file supplied by the Protein Data Bank. Instead of this section:

  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0

as with the other EDO ligands, EDO 207 has this section:

  2  4  1  0  0  0  0
  2  6  1  0  0  0  0
  6  8  1  0  0  0  0

The best thing we could do is to just give a warning if one of the downloaded ligands is invalid and press on. You can always amend it manually and re-add it to protein.ligands afterwards. I have pushed a commit now which should take care of that.

kexul commented 3 years ago

Thanks, it works perfectly!