dock-postprocess v0.2.0

dock-postprocess v0.2.0

This release adds explicit-solvent molecular dynamics support and expands force-field configuration throughout the OpenMM workflow.

Highlights

• Added dock-md for molecular dynamics with OpenMM
• NVT and NPT ensembles supported
• Controlled heating, equilibration, and production stages
• Explicit-solvent support with PME
• Vacuum (no-solvent) mode retained
• Configurable protein, ligand, and water force fields
• Protein support for ff14SB, ff19SB, and ff15ipq
• Ligand support for installed OpenFF and GAFF force fields
• Water models including TIP3P, TIP3P-FB, TIP4P-Ew, TIP4P-FB, SPC/E, OPC, and OPC3
• Configurable ionic strength, solvent padding, box shape, and nonbonded cutoff
• CUDA platform support
• MD trajectories, state reporting, checkpoints, final structures, and metadata
• Preserved support for receptor-specific residue variants and metal coordination restraints

Validation

See VALIDATION_0.2.0.md for validation details.

dock-postprocess v0.1.0

Initial public release of dock-postprocess.

Highlights:

• Standardized docking-workspace initialization with dock-init
• Native generalized OpenMM minimization
• Multichain receptor and ternary-complex support
• Configurable residue variants and metal restraints
• Post-minimization pose QC and optional focus-residue analysis
• Contact enrichment and interaction-landscape analysis
• Ligand conformational strain analysis
• Integrated master design table
• Stable L#### ligand identifiers and generalized results layout

The v0.1.0 workflow was regression-tested against the original validated p53/BRD4 workflow, including exact agreement in starting OpenMM potential energy for the minimizer validation case.

Some downstream analyses still use validated internal compatibility engines behind the generalized public interface.