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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Inconsistent output between 2.1.0 and 3.0.1 #164

Closed danny305 closed 3 years ago

danny305 commented 3 years ago

The following command works just fine with pdb2pqr2.1.1 whoever the equivalent command fails with the following error messages. 

pdb2pqr2.1.1
 os.system('python ./dependencies/pdb2pqr2.1/pdb2pqr.py --ff=parse --chain {} {}'.format(pdb_file, pqr_file))

pdb2pqr3.0.1
os.system(f'python ./dependencies/pdb2pqr-3.0.1/pdb2pqr.py --ff=PARSE --keep-chain {pdb_file} {pqr_file}')

# Error message when pdb_file = 3nir.pdb and pqr_file = 3nir.pqr.pdb

PQR SOFTWARE OUTPUT:
DEBUG:PDB2PQR3.0:Invoked with arguments: Namespace(alignment=None, apbs_input=None, assign_only=False, chains=None, clean=False, debump=True, display_coupled_residues=False, drop_water=False, ff='PARSE', ffout=None, filenames=[], grid=(0.0, 14.0, 0.1), include_header=False, input_path='./pdb_files/3nir.pdb', keep_chain=True, keep_protons=False, ligand=None, log_level='INFO', mutations=None, mutator=None, mutator_options=None, neutralc=False, neutraln=False, opt=True, output_pqr='./pdb_files/3nir.pqr.pdb', pH=7.0, pairene=1.0, parameters='/usr/local/lib/python3.7/site-packages/propka/propka.cfg', pdb2pka_out='pdb2pka_output', pdb2pka_resume=False, pdie=8.0, ph=7.0, pka_method=None, protonate_all=False, reference='neutral', reuse_ligand_mol2_file=False, sdie=80.0, thermophiles=None, titrate_only=None, userff=None, usernames=None, whitespace=False, window=(0.0, 14.0, 1.0))
DEBUG:PDB2PQR3.0:Args:  Namespace(alignment=None, apbs_input=None, assign_only=False, chains=None, clean=False, debump=True, display_coupled_residues=False, drop_water=False, ff='PARSE', ffout=None, filenames=[], grid=(0.0, 14.0, 0.1), include_header=False, input_path='./pdb_files/3nir.pdb', keep_chain=True, keep_protons=False, ligand=None, log_level='INFO', mutations=None, mutator=None, mutator_options=None, neutralc=False, neutraln=False, opt=True, output_pqr='./pdb_files/3nir.pqr.pdb', pH=7.0, pairene=1.0, parameters='/usr/local/lib/python3.7/site-packages/propka/propka.cfg', pdb2pka_out='pdb2pka_output', pdb2pka_resume=False, pdie=8.0, ph=7.0, pka_method=None, protonate_all=False, reference='neutral', reuse_ligand_mol2_file=False, sdie=80.0, thermophiles=None, titrate_only=None, userff=None, usernames=None, whitespace=False, window=(0.0, 14.0, 1.0))
INFO:PDB2PQR3.0:PDB2PQR v3.0 - biomolecular structure conversion software
INFO:PDB2PQR3.0:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO:PDB2PQR3.0:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO:PDB2PQR3.0:Checking and transforming input arguments.
DEBUG:pdb2pqr.input_output:Found DAT file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/parse.DAT
INFO:PDB2PQR3.0:Loading topology files.
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/AA.xml
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/NA.xml
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/PATCHES.xml
INFO:PDB2PQR3.0:Loading molecule: ./pdb_files/3nir.pdb
INFO:PDB2PQR3.0:Setting up molecule.
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom OG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Skipping atom reference for H1
DEBUG:pdb2pqr.aa:Ignoring atom H1
DEBUG:pdb2pqr.aa:Skipping atom reference for H2
DEBUG:pdb2pqr.aa:Ignoring atom H2
DEBUG:pdb2pqr.aa:Skipping atom reference for H3
DEBUG:pdb2pqr.aa:Ignoring atom H3
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG1
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom OG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG1
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG12
DEBUG:pdb2pqr.aa:Ignoring atom HG13
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom HD11
DEBUG:pdb2pqr.aa:Ignoring atom HD12
DEBUG:pdb2pqr.aa:Ignoring atom HD13
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG11
DEBUG:pdb2pqr.aa:Ignoring atom HG12
DEBUG:pdb2pqr.aa:Ignoring atom HG13
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom OD1
DEBUG:pdb2pqr.aa:Ignoring atom ND2
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom HD21
DEBUG:pdb2pqr.aa:Ignoring atom HD22
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom CD2
DEBUG:pdb2pqr.aa:Ignoring atom CE1
DEBUG:pdb2pqr.aa:Ignoring atom CE2
DEBUG:pdb2pqr.aa:Ignoring atom CZ
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom HD1
DEBUG:pdb2pqr.aa:Ignoring atom HD2
DEBUG:pdb2pqr.aa:Ignoring atom HE1
DEBUG:pdb2pqr.aa:Ignoring atom HE2
DEBUG:pdb2pqr.aa:Ignoring atom HZ
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom CD
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom HG2
DEBUG:pdb2pqr.aa:Ignoring atom HG3
DEBUG:pdb2pqr.aa:Ignoring atom HD2
DEBUG:pdb2pqr.aa:Ignoring atom HD3
DEBUG:pdb2pqr.aa:Skipping atom reference for CG
DEBUG:pdb2pqr.aa:Skipping atom reference for CD
DEBUG:pdb2pqr.aa:Skipping atom reference for HG2
DEBUG:pdb2pqr.aa:Skipping atom reference for HG3
DEBUG:pdb2pqr.aa:Skipping atom reference for HD2
DEBUG:pdb2pqr.aa:Skipping atom reference for HD3
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Skipping atom reference for HE2
DEBUG:pdb2pqr.aa:Skipping atom reference for CG
DEBUG:pdb2pqr.aa:Skipping atom reference for CD2
DEBUG:pdb2pqr.aa:Skipping atom reference for HB2
DEBUG:pdb2pqr.aa:Skipping atom reference for HB3
DEBUG:pdb2pqr.aa:Skipping atom reference for HG
DEBUG:pdb2pqr.aa:Skipping atom reference for HD21
DEBUG:pdb2pqr.aa:Skipping atom reference for HD22
DEBUG:pdb2pqr.aa:Skipping atom reference for HD23
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HD11
DEBUG:pdb2pqr.aa:Ignoring atom HD12
DEBUG:pdb2pqr.aa:Ignoring atom HD13
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom CD2
DEBUG:pdb2pqr.aa:Ignoring atom CD2
DEBUG:pdb2pqr.aa:Ignoring atom CE1
DEBUG:pdb2pqr.aa:Ignoring atom CE1
DEBUG:pdb2pqr.aa:Ignoring atom CE2
DEBUG:pdb2pqr.aa:Ignoring atom CE2
DEBUG:pdb2pqr.aa:Ignoring atom CZ
DEBUG:pdb2pqr.aa:Ignoring atom CZ
DEBUG:pdb2pqr.aa:Ignoring atom OH
DEBUG:pdb2pqr.aa:Ignoring atom OH
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom HD1
DEBUG:pdb2pqr.aa:Ignoring atom HD1
DEBUG:pdb2pqr.aa:Ignoring atom HD2
DEBUG:pdb2pqr.aa:Ignoring atom HD2
DEBUG:pdb2pqr.aa:Ignoring atom HE1
DEBUG:pdb2pqr.aa:Ignoring atom HE1
DEBUG:pdb2pqr.aa:Ignoring atom HE2
DEBUG:pdb2pqr.aa:Ignoring atom HE2
DEBUG:pdb2pqr.aa:Ignoring atom HH
DEBUG:pdb2pqr.aa:Ignoring atom HH
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Ignoring atom CD1
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG12
DEBUG:pdb2pqr.aa:Ignoring atom HG13
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom HD11
DEBUG:pdb2pqr.aa:Ignoring atom HD12
DEBUG:pdb2pqr.aa:Ignoring atom HD13
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA2
DEBUG:pdb2pqr.aa:Ignoring atom HA3
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB1
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom OG1
DEBUG:pdb2pqr.aa:Ignoring atom CG2
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB
DEBUG:pdb2pqr.aa:Ignoring atom HG1
DEBUG:pdb2pqr.aa:Ignoring atom HG21
DEBUG:pdb2pqr.aa:Ignoring atom HG22
DEBUG:pdb2pqr.aa:Ignoring atom HG23
DEBUG:pdb2pqr.aa:Ignoring atom N
DEBUG:pdb2pqr.aa:Ignoring atom CA
DEBUG:pdb2pqr.aa:Ignoring atom C
DEBUG:pdb2pqr.aa:Ignoring atom O
DEBUG:pdb2pqr.aa:Ignoring atom CB
DEBUG:pdb2pqr.aa:Ignoring atom CG
DEBUG:pdb2pqr.aa:Ignoring atom OD1
DEBUG:pdb2pqr.aa:Ignoring atom OD2
DEBUG:pdb2pqr.aa:Ignoring atom H
DEBUG:pdb2pqr.aa:Ignoring atom HA
DEBUG:pdb2pqr.aa:Ignoring atom HB2
DEBUG:pdb2pqr.aa:Ignoring atom HB3
DEBUG:pdb2pqr.aa:Skipping atom reference for HD2
DEBUG:pdb2pqr.aa:Ignoring atom HD2
DEBUG:pdb2pqr.aa:Skipping atom reference for OXT
DEBUG:pdb2pqr.protein:Parsing EOH as new residue
DEBUG:pdb2pqr.protein:Parsing EOH as new residue
DEBUG:pdb2pqr.protein:Parsing EOH as new residue
DEBUG:pdb2pqr.protein:Parsing EOH as new residue
INFO:PDB2PQR3.0:Created protein object with 148 residues and 765 atoms.
WARNING:PDB2PQR3.0:Multiple occupancies found: N in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: CA in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: C in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: O in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: CB in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: OG1 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: CG2 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: H1 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: H2 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: H3 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HA in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HB in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HG1 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HG21 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HG22 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found: HG23 in THR A 1.
WARNING:PDB2PQR3.0:Multiple occupancies found in THR A 1. At least one of the instances is being ignored.
WARNING:PDB2PQR3.0:Multiple occupancies found: N in THR A 2.
WARNING:PDB2PQR3.0:Multiple occupancies found: CA in THR A 2.
WARNING:pdb2pqr.input_output:Suppressing further 'Multiple occupancies found' messages
INFO:PDB2PQR3.0:Setting termini states for protein chains.
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 1 patched with NTERM
DEBUG:pdb2pqr.protein:PATCH INFO: ASN A 46 patched with CTERM
DEBUG:pdb2pqr.protein:Done setting termini.
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 2 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 3 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 4 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: PRO A 5 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: SER A 6 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ILE A 7 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: VAL A 8 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ALA A 9 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ARG A 10 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: SER A 11 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ASN A 12 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: PHE A 13 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ASN A 14 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: VAL A 15 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 16 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ARG A 17 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: LEU A 18 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: PRO A 19 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: GLY A 20 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 21 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: SER A 22 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: GLU A 23 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ALA A 24 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ILE A 25 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 26 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ALA A 27 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 28 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: TYR A 29 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 30 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: GLY A 31 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 32 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ILE A 33 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ILE A 34 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ILE A 35 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: PRO A 36 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: GLY A 37 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ALA A 38 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: THR A 39 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 40 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: PRO A 41 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: GLY A 42 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ASP A 43 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: TYR A 44 patched with PEPTIDE
DEBUG:pdb2pqr.protein:PATCH INFO: ALA A 45 patched with PEPTIDE
INFO:PDB2PQR3.0:Loading forcefield.
DEBUG:pdb2pqr.input_output:Found DAT file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/parse.DAT
DEBUG:pdb2pqr.input_output:Found NAMES file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/parse.NAMES
INFO:PDB2PQR3.0:Loading hydrogen topology definitions.
DEBUG:pdb2pqr.input_output:Found DAT file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/HYDROGENS.xml
INFO:PDB2PQR3.0:This biomolecule is clean.  No repair needed.
INFO:PDB2PQR3.0:Updating disulfide bridges.
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 3 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 3 - CYS A 40
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 4 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 4 - CYS A 32
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 16 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 16 - CYS A 26
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 26 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 26 - CYS A 16
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 32 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 32 - CYS A 4
DEBUG:pdb2pqr.protein:PATCH INFO: CYS A 40 patched with CYX
DEBUG:pdb2pqr.protein:CYS A 40 - CYS A 3
INFO:PDB2PQR3.0:Debumping biomolecule.
Traceback (most recent call last):
  File "./dependencies/pdb2pqr-3.0.1/pdb2pqr.py", line 23, in <module>
    main(args)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/main.py", line 578, in main
    is_cif=is_cif)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/main.py", line 439, in non_trivial
    debumper.debump_protein()
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/debump.py", line 130, in debump_protein
    self.protein.set_reference_distance()
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/protein.py", line 440, in set_reference_distance
    atom.refdistance = len(util.shortest_path(map_, atom, caatom)) - 1
TypeError: object of type 'NoneType' has no len()

# Error message when pdb_file=3m24_final_tot.pdb and pqr_file=3m24_final_tot.pqr.pdb
# Where final_tot means the rcsb pdb file has been ran through the PDB-redo server. 

PQR SOFTWARE OUTPUT:
DEBUG:PDB2PQR3.0:Invoked with arguments: Namespace(alignment=None, apbs_input=None, assign_only=False, chains=None, clean=False, debump=True, display_coupled_residues=False, drop_water=False, ff='PARSE', ffout=None, filenames=[], grid=(0.0, 14.0, 0.1), include_header=False, input_path='./pdb_files/3m24_final_tot.pdb', keep_chain=True, keep_protons=False, ligand=None, log_level='INFO', mutations=None, mutator=None, mutator_options=None, neutralc=False, neutraln=False, opt=True, output_pqr='./pdb_files/3m24_final_tot.pqr.pdb', pH=7.0, pairene=1.0, parameters='/usr/local/lib/python3.7/site-packages/propka/propka.cfg', pdb2pka_out='pdb2pka_output', pdb2pka_resume=False, pdie=8.0, ph=7.0, pka_method=None, protonate_all=False, reference='neutral', reuse_ligand_mol2_file=False, sdie=80.0, thermophiles=None, titrate_only=None, userff=None, usernames=None, whitespace=False, window=(0.0, 14.0, 1.0))
DEBUG:PDB2PQR3.0:Args:  Namespace(alignment=None, apbs_input=None, assign_only=False, chains=None, clean=False, debump=True, display_coupled_residues=False, drop_water=False, ff='PARSE', ffout=None, filenames=[], grid=(0.0, 14.0, 0.1), include_header=False, input_path='./pdb_files/3m24_final_tot.pdb', keep_chain=True, keep_protons=False, ligand=None, log_level='INFO', mutations=None, mutator=None, mutator_options=None, neutralc=False, neutraln=False, opt=True, output_pqr='./pdb_files/3m24_final_tot.pqr.pdb', pH=7.0, pairene=1.0, parameters='/usr/local/lib/python3.7/site-packages/propka/propka.cfg', pdb2pka_out='pdb2pka_output', pdb2pka_resume=False, pdie=8.0, ph=7.0, pka_method=None, protonate_all=False, reference='neutral', reuse_ligand_mol2_file=False, sdie=80.0, thermophiles=None, titrate_only=None, userff=None, usernames=None, whitespace=False, window=(0.0, 14.0, 1.0))
INFO:PDB2PQR3.0:PDB2PQR v3.0 - biomolecular structure conversion software
INFO:PDB2PQR3.0:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO:PDB2PQR3.0:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO:PDB2PQR3.0:Checking and transforming input arguments.
DEBUG:pdb2pqr.input_output:Found DAT file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/parse.DAT
INFO:PDB2PQR3.0:Loading topology files.
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/AA.xml
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/NA.xml
DEBUG:pdb2pqr.input_output:Found xml file /mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/dat/PATCHES.xml
INFO:PDB2PQR3.0:Loading molecule: ./pdb_files/3m24_final_tot.pdb
Traceback (most recent call last):
  File "./dependencies/pdb2pqr-3.0.1/pdb2pqr.py", line 23, in <module>
    main(args)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/main.py", line 559, in main
    pdblist, is_cif = io.get_molecule(args.input_path)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/input_output.py", line 332, in get_molecule
    pdblist, errlist = pdb.read_pdb(input_file)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/pdb.py", line 1910, in read_pdb
    obj = klass(line)
  File "/mutcompute/dependencies/pdb2pqr-3.0.1/pdb2pqr/pdb.py", line 820, in __init__
    self.mod_num = int(str.strip(line[43:46]))
ValueError: invalid literal for int() with base 10: ''

I am running this in a python3 docker container so I can't revert to using pdb2pqr2.1.

I can provide the raw pdb files if needed.

I am going to try to debug this but I thought I should let you guys know!

danny305 commented 3 years ago

to be clear. both the of these files (3nir.pdb and 3m24_final_tot.pdb work just fine in 2.1.1

danny305 commented 3 years ago

Here are the pdb files:

pdb_files.tar.gz

sobolevnrm commented 3 years ago

There are many changes in PDB2PQR since 2.1.1; we've just updated the document with a summary of these changes.

The 3nir.pdb "works" with the latest version (3.1.0, released last week) of PDB2PQR: the program fails gracefully when it encounters a gap in the backbone.

The 3m24_final_tot.pdb fails with 3.1.0 because of CISPEP and CRYST1 records that don't comply with the PDB format. However, it does not fail very gracefully--and probably shouldn't fail at all since this information isn't essential for the PDB2PQR functionality. I'll create a new issue to fix this.