Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Electrostatics/pdb2pqr issues and pull requests
#400 - Comparing web server output and Command line output
Issue -
State: closed - Opened by HaydenGJ about 2 months ago
#399 - Protonation of nonstandard residues not occurring
Issue -
State: open - Opened by HeheHahaHoHoHo 2 months ago
- 2 comments
#398 - Issue using APBS plugin on polysaccharides
Issue -
State: open - Opened by NoaBinnes 3 months ago
#397 - HIP residues getting renamed to HI+ using the pip tool
Issue -
State: closed - Opened by beta-sheet 3 months ago
#396 - Getting CRITICAL:Found gap in biomolecule structure for atom
Issue -
State: open - Opened by Tonylac77 4 months ago
#394 - Ligand amide bond type not
Issue -
State: open - Opened by and-tos 5 months ago
- 1 comment
#393 - Pending Job Start
Issue -
State: open - Opened by hillaryhe 5 months ago
- 6 comments
#392 - pdb2pqr does not remove atoms as expected
Issue -
State: open - Opened by CyberCatQ 7 months ago
#391 - Adding pKa-ANI as an option to assign titratable states
Pull Request -
State: open - Opened by sastrys1 7 months ago
- 4 comments
#389 - Using pKa-ANI to compute titration states at a given pH?
Issue -
State: open - Opened by sastrys1 7 months ago
- 2 comments
#388 - What to do when I have multiple occupancies?
Issue -
State: closed - Opened by mysecondnameisdanger 7 months ago
#387 - Fix mol2 parsing
Pull Request -
State: open - Opened by nimijkrap 8 months ago
- 1 comment
#386 - Error to process neutral Cter of ASN
Issue -
State: open - Opened by micmar15sr 8 months ago
- 2 comments
#385 - Update Sphinx versions.
Pull Request -
State: closed - Opened by sobolevnrm 9 months ago
- 1 comment
#384 - Upgrade Sphinx packages
Issue -
State: closed - Opened by sobolevnrm 9 months ago
#383 - Allow hexadecimal ATOM id
Pull Request -
State: open - Opened by SSchott 9 months ago
#382 - Add tests for failed titration state naming
Pull Request -
State: closed - Opened by sobolevnrm 9 months ago
- 2 comments
#381 - Non-integer residue charge with PEOEPB
Issue -
State: open - Opened by sobolevnrm 9 months ago
#380 - Generate tests for amino acid naming
Issue -
State: closed - Opened by sobolevnrm 9 months ago
- 1 comment
#379 - Version 3.6.2 release candidate
Pull Request -
State: closed - Opened by sobolevnrm 9 months ago
- 4 comments
#378 - Update pkg_resources
Issue -
State: closed - Opened by sobolevnrm 9 months ago
- 1 comment
#377 - Release new version
Issue -
State: closed - Opened by sobolevnrm 9 months ago
#376 - Error in ligand processing
Issue -
State: open - Opened by adventureneed 10 months ago
- 2 comments
#375 - inputget error on alphafold structures
Issue -
State: open - Opened by shaharsu 10 months ago
- 2 comments
#374 - Caculating electrrostatic potential over distance
Issue -
State: open - Opened by hanahg 10 months ago
- 4 comments
#373 - pdb2pqr modifies the chain names
Issue -
State: open - Opened by ndonyapour 10 months ago
- 4 comments
#372 - Fix `io.test_for_file` failing for editable installs
Pull Request -
State: closed - Opened by sphuber 12 months ago
- 1 comment
#371 - update docutils please?
Issue -
State: open - Opened by pgbarletta about 1 year ago
#370 - Allow using hexadecimal ATOM id
Pull Request -
State: closed - Opened by SSchott about 1 year ago
- 5 comments
#369 - ValueError: 'P' is not in list
Issue -
State: open - Opened by GuhLelouch about 1 year ago
- 2 comments
#368 - Too far hydrogen generated from "charmmgui corrected" pdb?
Issue -
State: open - Opened by jdandrade-gmx about 1 year ago
- 3 comments
#367 - Replace XML-format data files with YAML
Issue -
State: open - Opened by sobolevnrm about 1 year ago
#366 - Warn about unused PROPKA options
Pull Request -
State: closed - Opened by sobolevnrm about 1 year ago
- 1 comment
#365 - Add code warnings and documentation about the --keep-protons option being ignored
Issue -
State: closed - Opened by dargen3 over 1 year ago
- 1 comment
#364 - Fix broken link in "Other software docs"
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 1 comment
#363 - Fix typo in visualization documentation
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#362 - Validation of protonation states in the output PDB File
Issue -
State: closed - Opened by samit1194 over 1 year ago
- 1 comment
#361 - Error message heavy atoms missing
Issue -
State: closed - Opened by bakpaotlrasin over 1 year ago
- 1 comment
#360 - producing pqr file for ligand only (not protein) - error message: ValueError: 'P' is not in list
Issue -
State: open - Opened by evelyne-deplazes over 1 year ago
- 5 comments
#359 - Residues being renamed TER
Issue -
State: closed - Opened by quockerwodger over 1 year ago
- 1 comment
#358 - naming inconsistency with CHARMM
Issue -
State: open - Opened by pokhreln over 1 year ago
- 6 comments
#357 - Pending job start
Issue -
State: open - Opened by axm8099 over 1 year ago
- 4 comments
#355 - chelation sites
Issue -
State: closed - Opened by joaomcteixeira over 1 year ago
#353 - There are concatenated fields in PQR output
Issue -
State: closed - Opened by wt12318 over 1 year ago
- 1 comment
#352 - Version 3.6.1 release candidate.
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 3 comments
#351 - Update copyright to 2023.
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 2 comments
#350 - Nathan/348
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 2 comments
#349 - Release PDB2PQR 3.6.1
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
- 1 comment
#348 - Fix broken PDB2PQR documentation
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#346 - hydrogen atoms with zero radius ?!
Issue -
State: closed - Opened by UnixJunkie over 1 year ago
- 1 comment
#345 - PDB2PQR 3.6.0 release candidate.
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 2 comments
#344 - Update copyright date to 2023
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#343 - Update ChangeLog with modifications since last release.
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 2 comments
#342 - Need to update PDB2PQR Python compatibility.
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#341 - Update to PROPKA 3.5
Pull Request -
State: closed - Opened by sobolevnrm over 1 year ago
- 3 comments
#340 - Update ChangeLog with changes since last release
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#339 - Update `setup.py` to force latest version of PROPKA
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
#338 - Run pdb2pqr as python library
Issue -
State: open - Opened by dargen3 over 1 year ago
- 1 comment
#337 - Another no PQR file in outputs issue
Issue -
State: open - Opened by lbizzio over 1 year ago
- 1 comment
#336 - tetrahedral hydrogen reconstruction issue
Issue -
State: open - Opened by sunghh44 over 1 year ago
#335 - New PDB2PQR release
Issue -
State: closed - Opened by sobolevnrm over 1 year ago
- 12 comments
#334 - Possible race condition in main.run_propka()
Issue -
State: open - Opened by bradakta over 1 year ago
- 3 comments
#333 - Problems with Mn ion in enzyme
Issue -
State: closed - Opened by mverissi over 1 year ago
- 1 comment
#332 - PDB2PQR generates misaligned residue names for GLU (and possibly others)
Issue -
State: open - Opened by sobolevnrm almost 2 years ago
#331 - format problems
Issue -
State: open - Opened by pineappleXmen almost 2 years ago
- 1 comment
#330 - Removed redundant ChangeLog file.
Pull Request -
State: closed - Opened by sobolevnrm almost 2 years ago
#329 - Remove ChangeLog.md
Issue -
State: closed - Opened by sobolevnrm almost 2 years ago
#327 - missing modified phosphorylated threonine residue (THP1)
Issue -
State: closed - Opened by sau1978 about 2 years ago
#326 - waiting for Pending Job Start too long
Issue -
State: closed - Opened by Eridium1 about 2 years ago
- 1 comment
#325 - Ligand with Amide Bonds
Issue -
State: closed - Opened by GeorgianaLiang about 2 years ago
- 3 comments
#324 - `Got code 404 while retrieving https://files.rcsb.org/download/PARSE.pdb` while using PARSE forcefield
Issue -
State: closed - Opened by ljmartin about 2 years ago
- 3 comments
#323 - phospholipid problems
Issue -
State: open - Opened by corbinsblack about 2 years ago
#322 - Protonation of histidine
Issue -
State: closed - Opened by kexul about 2 years ago
- 1 comment
#321 - OPM and pdb2pqr
Issue -
State: open - Opened by khelmy55 about 2 years ago
- 5 comments
#320 - Cannot add --display-coupled-residues flag to PDB2PQR webserver
Issue -
State: closed - Opened by rediaz111 over 2 years ago
- 1 comment
#319 - Biomolecue charge is non-integer --- pdb:4yki
Issue -
State: closed - Opened by khelmy55 over 2 years ago
- 1 comment
#318 - server stuck
Issue -
State: closed - Opened by sunimei3 over 2 years ago
- 8 comments
#316 - use pd2pqr in python3 script
Issue -
State: closed - Opened by EtienneReboul over 2 years ago
- 4 comments
#315 - Eliminated need to write to temporary file in disk
Pull Request -
State: closed - Opened by mimminou over 2 years ago
- 2 comments
#314 - A bug of creating the Biomolecule instance
Issue -
State: open - Opened by chemsh over 2 years ago
#313 - error during conversion of pdb file to pqr file format
Issue -
State: open - Opened by rubinanoor9 over 2 years ago
- 2 comments
#312 - Error reading four letters residues
Issue -
State: closed - Opened by alexmcff over 2 years ago
- 1 comment
#311 - atomic radius
Issue -
State: closed - Opened by lex1213 over 2 years ago
- 1 comment
#307 - Cyclic peptide support
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 2 comments
#306 - Issue with cyclic peptides
Issue -
State: closed - Opened by stefdoerr over 2 years ago
#305 - Rename radian-to-degree constant
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 1 comment
#304 - Hydrogen addition problems with non-experimental input structures
Issue -
State: open - Opened by dargen3 over 2 years ago
- 19 comments
#303 - CIF Read Error: AttributeError: 'NoneType' object has no attribute 'get_value'
Issue -
State: closed - Opened by jacob-r-anderson over 2 years ago
- 2 comments
#302 - AttributeError: 'NoneType' object has no attribute 'group_type'
Issue -
State: closed - Opened by Aunity over 2 years ago
- 6 comments
#301 - Fix issues in protonated terminal residue naming
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 3 comments
#300 - NMR proteins with hydrogens fail preparation
Issue -
State: open - Opened by stefdoerr over 2 years ago
- 3 comments
#299 - Missing heavy atoms error erroring
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 1 comment
#298 - Fix critical bug in python 3.8+ versions with temporary file creation
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 12 comments
#297 - Maintain original chain names unless there is a break
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 3 comments
#296 - Adding hydrogens to residue with charged first atom creates charged hydrogens
Issue -
State: open - Opened by stefdoerr over 2 years ago
- 1 comment
#295 - Set up new version (3.5.2)
Pull Request -
State: closed - Opened by sobolevnrm over 2 years ago
- 1 comment
#294 - XML parser fix
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
#293 - Problem with DefinitionHandler
Issue -
State: closed - Opened by stefdoerr over 2 years ago
#292 - New PDB2PQR release
Issue -
State: closed - Opened by sobolevnrm over 2 years ago
- 7 comments
#291 - Fix bug and add support for integer resnames which exist in PDB
Pull Request -
State: closed - Opened by stefdoerr over 2 years ago
- 4 comments