openmmtools: Release 0.8.0

Added a host-guest system (CB7:B2): HostGuestVacuum HostGuestImplicit HostGuestExplicit GHMCIntegrator now includes protection from nan

choderalab/openmmtools: Release 0.8.3 - minor feature update

This release extends some of the systems in openmmtools.testsystems to allow multiple CustomGBForce-based GB models supported by OpenMM's customgbforces.py functionality to be used. TolueneImplicit, HostGuestImplicit, and LysozymeImplicit now accept the implicitSolvent option, allowing GB models from simtk.openmm.app (such as HCT, OBC1, OBC2, GBn, and GBn2) to be optionally specified. OBC1 remains the default. These three classes also support any kwargs supported by AmberPrmtopFile.createSystem(). Any parameters that createSystem supports will be passed along from the constructor. TolueneImplicit and HostGuestImplicit also have variants like TolueneImplicitHCT, TolueneImplicitOBC1, etc. for all OpenMM-supported implicit solvent models

choderalab/openmmtools: Bugfix release 0.9.1

This release fixes a Python 2 bug caused by how Python 2 and Python 3 handle differently user-defined equality operators. This was affecting the sanity checks in alchemy.AlchemicalState to always fail when checking the compatibility of a System

choderalab/openmmtools: 0.13.1 - Bugfix release

In this release: Fix pickling of CompoundThermodynamicState (#284). Add missing term to OBC2 GB alchemical Force (#288). Generalize forcefactories.restrain_atoms() to non-protein receptors (#290). Standardize integrator global variables in ContextCache (#291)

choderalab/openmoltools: Service release

This is a bugfix maintenance release featuring the following changes: Add option to use alternate leaprc to run_tleap Allow option to skip checking force parameters of impropers. Add additional debug info to system checker for harmonic angle

choderalab/openmoltools: v0.8.0

This release: Removes acpype, which had been deprecated Changes license to MIT Implements new charging routine from OpenEye while maintaining legacy charging as an option Makes minor maintenance changes to Epik Allows standardization of water names (such as to allow proper water recognition via MDTraj

choderalab/openmoltools: default charging, bondtypes and mdtraj compatibility

This release: update as mdtraj.topology.from_dataframe now returns four values using OEAM1BCCELF10Charges as default, with OEAM1BCCCharges fallback using bondtype instead of antechamber to avoid antechamber valency complaint