Issues

• [Docs]: Update Conda Installation Path within Docs

  documentationenhancement
  Task

  CCPBioSim/prepmd#42 · Filter by author harryswift01 opened on Sep 15, 2026
  

• Remove duplicated logo from README.md

  bug
  Task

  CCPBioSim/prepmd#40 · Filter by author harryswift01 opened on Sep 7, 2026
  

• Certain structures fail because the _entity_poly_seq entry in the mmcif file does not contain the full sequence

  CCPBioSim/prepmd#37 · Filter by author Rob-Welch opened on Aug 27, 2026
  1

• Add an option to cap termini with missing residues

  CCPBioSim/prepmd#30 · Filter by author jthorton opened on Jul 8, 2026
  1

• PDBFixer only code path produces poorly-formatted cif files

  CCPBioSim/prepmd#29 · Filter by author Rob-Welch opened on Jul 7, 2026
  1

• CI should also test conda install

  CCPBioSim/prepmd#28 · Filter by author Rob-Welch opened on Jul 7, 2026

• OpenMM can't write OpenFF topologies; OpenFF can't write .mmcif files

  CCPBioSim/prepmd#12 · Filter by author Rob-Welch opened on May 11, 2026

• Can't build or install on windows due to openff/ambertools dependency

  CCPBioSim/prepmd#11 · Filter by author Rob-Welch opened on Apr 20, 2026

• MDAnalysis can't read and write mmCif files

  CCPBioSim/prepmd#10 · Filter by author Rob-Welch opened on Apr 20, 2026

• conda pdb2pqr package is outdated, possibly unmaintained

  CCPBioSim/prepmd#9 · Filter by author Rob-Welch opened on Apr 20, 2026

• VMD can't read mmCif files generated by OpenMM

  CCPBioSim/prepmd#7 · Filter by author Rob-Welch opened on Dec 12, 2025