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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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`Got code 404 while retrieving https://files.rcsb.org/download/PARSE.pdb` while using PARSE forcefield #324

Closed ljmartin closed 1 year ago

ljmartin commented 1 year ago

Hi PDB2PQR, I'd like to use the pdb2pqr30 to add neutral terminal caps to a PDB. It appears the link given to the PARSE.pdb file points to the wrong place. On running:

pdb2pqr30 -ff PARSE --neutralc --neutraln myfile.pdb

a 404 is returned:

OSError: Got code 404 while retrieving https://files.rcsb.org/download/PARSE.pdb

I couldn't find PARSE.pdb in ftp://files.rcsb.org/ - is there an up to date link somewhere? Thanks

sobolevnrm commented 1 year ago

It looks like you are missing a dash in the --ff option as well as an output PQR path. You should try something like:

pdb2pqr30 -off PARSE --neutralc --neutraln myfile.pdb myfile.pqr
ljmartin commented 1 year ago

Thanks @sobolevnrm, but I'm not sure that addresses the issue. Pip-installed pdb2pqr30 (as installed per the docs) has input:

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

i.e. using flag --ff. Using the command above returns pdb2pqr: error: argument -o/--pH: invalid float value: 'ff' Perhaps the pip version is an older version? pdb2pqr30 --version reports pdb2pqr 3.5.2.

sobolevnrm commented 1 year ago

Oops -- I had a typo above. Sorry!

Please try:

pdb2pqr30 --ff PARSE --neutralc --neutraln myfile.pdb myfile.pqr

Note the use of two dashes instead of one.