PDB2PQR30(1)

🎀 PDB2PQR30(1) 🎀

okay bestie, welcome to the pdb2pqr30 manual page — that's section 1 of the user commands, and yes it's giving main character energy ✨

---

💖 NAME 💖

pdb2pqr30 — the manual page for pdb2pqr30 version 3.6.1+dfsg 🫶

---

🌸 DESCRIPTION 🌸

bestie. sit down. this is the biomolecular structure conversion software, PDB2PQR v3.6.1. no cap. 💅

here's the usage line, verbatim, don't touch it:

usage: pdb2pqr [-h] [--ff {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}]
       [--userff USERFF] [--clean] [--nodebump] [--noopt] [--keep-chain]
       [--assign-only] [--ffout
       {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}] [--usernames
       USERNAMES] [--apbs-input APBS_INPUT] [--pdb-output PDB_OUTPUT]
       [--ligand LIGAND] [--whitespace] [--neutraln] [--neutralc]
       [--drop-water] [--include-header] [--titration-state-method
       {propka}] [--with-ph PH] [-f FILENAMES] [-r REFERENCE] [-c
       CHAINS] [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m
       MUTATIONS] [-p PARAMETERS] [--log-level
       {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW
       WINDOW] [-g GRID GRID GRID] [--mutator MUTATOR] [--mutator-option
       MUTATOR_OPTIONS] [-d] [-l] [-k] [-q] [--protonate-all]
       [--version] input_path output_pqr

---

🦋 positional arguments 🦋

these two are the moment, the whole point, the it-girls of the command line:

• input_path — the input PDB path, or an ID so it gets fetched from the RCSB database 💜
• output_pqr — where the output PQR goes 🎀

---

⭐ options ⭐

• -h, --help — show this help message and exit. classic. iconic. she tells you everything 🫶
• --version — show the program's version number and exit 💅

---

👑 Mandatory options 👑

listen, bestie, one of the following options must be used. it's not a vibe, it's a rule. periodt.

• --ff {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON} — the forcefield to use. (default: PARSE) ⚡
• --userff USERFF — the user-created forcefield file to use. requires --usernames and overrides --ff (default: None)
• --clean — do no optimization, atom addition, or parameter assignment — just return the original PDB file in aligned format. overrides --ff and --userff (default: False). it's giving "no thoughts, head empty, just give me the file back" 💀

---

🌈 General options 🌈

• --nodebump — do not perform the debumping operation (default: True)
• --noopt — do not perform hydrogen optimization (default: True)
• --keep-chain — keep the chain ID in the output PQR file (default: False)
• --assign-only — only assign charges and radii — do not add atoms, debump, or optimize. (default: False)
• --ffout {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON} — instead of using the standard canonical naming scheme for residue and atom names, use the names from the given forcefield (default: None)
• --usernames USERNAMES — the user-created names file to use. required if using --userff (default: None)
• --apbs-input APBS_INPUT — create a template APBS input file based on the generated PQR file, at the specified location. (default: None) 🧚
• --pdb-output PDB_OUTPUT — create a PDB file based on input. this one will be missing charges and radii (default: None)
• --ligand LIGAND — calculate the parameters for a single MOL2-format ligand at the path specified by this option. the MOL2 ligand name should match only one ligand in the PDB file. (default: None)
• --whitespace — insert whitespaces between atom name and residue name, between x and y, and between y and z. (default: False) ✨
• --neutraln — make the N-terminus of a protein neutral (default is charged). requires the PARSE force field. (default: False)
• --neutralc — make the C-terminus of a protein neutral (default is charged). requires the PARSE force field. (default: False)
• --drop-water — drop waters before processing the biomolecule. (default: False) 💧
• --include-header — include the PDB header in the PQR file.

⚠️ WARNING: the resulting PQR file will not work with APBS versions prior to 1.5 (default: False)

---

💜 pKa options 💜

these are the options for titration calculations, bestie 🧪

• --titration-state-method {propka} — method used to calculate titration states. if a titration state method is selected, titratable residue charge states will be set by the pH value supplied by --with_ph (default: None)
• --with-ph PH — pH values to use when applying the results of the selected pH calculation method. (default: 7.0)

---

🍓 PROPKA invocation options 🍓

• -f FILENAMES, --file FILENAMES — read data from <filename>, i.e. <filename> is added to arguments (default: [])
• -r REFERENCE, --reference REFERENCE — setting which reference to use for stability calculations [neutral/low-pH] (default: neutral)
• -c CHAINS, --chain CHAINS — creating the protein with only a specified chain. specify " " for chains without an ID [all] (default: None)
• -i TITRATE_ONLY, --titrate_only TITRATE_ONLY — treat only the specified residues as titratable. the value should be a comma-separated list of "chain:resnum" values; for example: -i "A:10,A:11" (default: None)
• -t THERMOPHILES, --thermophile THERMOPHILES — defining a thermophile filename; usually used in 'alignment-mutations' (default: None)
• -a ALIGNMENT, --alignment ALIGNMENT — alignment file connecting <filename> and <thermophile> [<thermophile>.pir] (default: None)
• -m MUTATIONS, --mutation MUTATIONS — specifying mutation labels, which is used to modify <filename> according to, e.g. N25R/N181D (default: None)
• -p PARAMETERS, --parameters PARAMETERS — set the parameter file [{default:s}] (default: /usr/lib/python3/dist-packages/propka/propka.cfg)
• --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} — logging level verbosity (default: INFO)
• -o PH, --pH PH — setting the pH-value used in e.g. stability calculations [7.0] (default: 7.0)
• -w WINDOW WINDOW WINDOW, --window WINDOW WINDOW WINDOW — setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0] (default: (0.0, 14.0, 1.0))
• -g GRID GRID GRID, --grid GRID GRID GRID — setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1] (default: (0.0, 14.0, 0.1))
• --mutator MUTATOR — setting the approach for mutating <filename> [alignment/scwrl/jackal] (default: None)
• --mutator-option MUTATOR_OPTIONS — setting a property for the mutator [e.g. type="side-chain"] (default: None)
• -d, --display-coupled-residues — displays alternative pKa values due to coupling of titratable groups (default: False)
• -l, --reuse-ligand-mol2-files — reuses the ligand mol2 files, allowing the user to alter ligand bond orders (default: False)
• -k, --keep-protons — keep protons in the input file (default: False)
• -q, --quiet — suppress non-warning messages (default: None) 🤫
• --protonate-all — protonate all atoms (will not influence pKa calculation) (default: False)

---

and that's the whole page, bestie 💖 this was pdb2pqr30 version 3.6.1+dfsg, dated June 2023, and you read it in the PDB2PQR30(1) era — go convert some biomolecules, you absolute icon 🎀✨🦋👑