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Ligands still don't always end up in the right place

Status: Open.

#15 In CCPBioSim/prepmd;

· Rob-Welch opened on May 21, 2026

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

Status: Open.

#12 In CCPBioSim/prepmd;

· Rob-Welch opened on May 11, 2026

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

Status: Open.

#11 In CCPBioSim/prepmd;

· Rob-Welch opened on Apr 20, 2026

MDAnalysis can't read and write mmCif files

Status: Open.

#10 In CCPBioSim/prepmd;

· Rob-Welch opened on Apr 20, 2026

conda pdb2pqr package is outdated, possibly unmaintained

Status: Open.

#9 In CCPBioSim/prepmd;

· Rob-Welch opened on Apr 20, 2026

VMD can't read mmCif files generated by OpenMM

Status: Open.

#7 In CCPBioSim/prepmd;

· Rob-Welch opened on Dec 12, 2025