Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Inconsistent output between 2.1.0 and 3.0.1 #164

Closed
danny305 opened this issue Dec 21, 2020 · 3 comments
Closed

Inconsistent output between 2.1.0 and 3.0.1 #164

danny305 opened this issue Dec 21, 2020 · 3 comments

Comments

@danny305
Copy link

danny305 commented Dec 21, 2020 •
edited
Loading

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
Copy link
Author

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

@danny305
Copy link
Author

Here are the pdb files:

pdb_files.tar.gz

@sobolevnrm
Copy link
Member

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.

@sobolevnrm sobolevnrm mentioned this issue Dec 27, 2020
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@sobolevnrm @danny305