search

marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
95 stars 43 forks source link

Error While Martinizing "AssertionError" #592

Open Harshitasahni opened 5 months ago

Harshitasahni commented 5 months ago

INFO - general - Read 1 molecules from PDB file frame_50001.pdb INFO - step - Guessing the bonds. INFO - general - 8 molecules after guessing bonds INFO - step - Repairing the graph. INFO - general - Applying modification N-ter to residue A-ASN1 INFO - general - Applying modification N-ter to residue A-LEU2 INFO - general - Applying modification C-ter to residue A-GLY10 INFO - missing-atom - Missing atom ILE4:CD INFO - missing-atom - Missing atom GLY10:OXT INFO - general - Applying modification N-ter to residue A-SER13 INFO - general - Applying modification C-ter to residue A-GLY15 INFO - missing-atom - Missing atom GLY15:OXT INFO - general - Applying modification N-ter to residue A-ARG16 INFO - general - Applying modification C-ter to residue A-PRO17 INFO - missing-atom - Missing atom PRO17:OXT INFO - step - Dealing with modifications. WARNING - unknown-input - Could not identify the modifications for residues [], involving atoms ['70-CD1'] INFO - general - Identified the modifications ['N-ter'] on residues ['ASN1', 'ASN1', 'ASN1', 'ASN1'] INFO - general - Identified the modifications ['N-ter'] on residues ['LEU2', 'LEU2', 'LEU2', 'LEU2', 'TYR3'] INFO - general - Identified the modifications ['C-ter'] on residues ['ASP9', 'GLY10', 'GLY10', 'GLY10'] INFO - general - Identified the modifications ['N-ter'] on residues ['SER13', 'SER13', 'SER13', 'SER13', 'SER14'] INFO - general - Identified the modifications ['C-ter'] on residues ['SER14', 'GLY15', 'GLY15', 'GLY15'] INFO - general - Identified the modifications ['N-ter'] on residues ['ARG16', 'ARG16', 'ARG16', 'ARG16', 'PRO17'] Traceback (most recent call last): File "/users/sahni/.local/bin/martinize2", line 1110, in entry() File "/users/sahni/.local/bin/martinize2", line 874, in entry system = pdb_to_universal( File "/users/sahni/.local/bin/martinize2", line 157, in pdb_to_universal vermouth.CanonicalizeModifications().run_system(canonicalized) File "/users/sahni/.local/lib/python3.10/site-packages/vermouth/processors/processor.py", line 37, in run_system mols.append(self.run_molecule(molecule)) File "/users/sahni/.local/lib/python3.10/site-packages/vermouth/processors/canonicalize_modifications.py", line 381, in run_molecule fix_ptm(molecule) File "/users/sahni/.local/lib/python3.10/site-packages/vermouth/processors/canonicalize_modifications.py", line 312, in fix_ptm identified = identify_ptms(residue, res_ptms, options) File "/users/sahni/.local/lib/python3.10/site-packages/vermouth/processors/canonicalize_modifications.py", line 178, in identify_ptms assert len(match) == 1 AssertionError

pckroon commented 5 months ago

That's indeed not supposed to happen. What's your command line invocation to reach this? Which version of martinize2?