Perses

Published June 26, 2022 | Version 0.10.1

Software Open

0.10.1 - Release

Bugfix release.

Bugfixes

Bug when trying to use the new RESTCapableHybridTopologyFactory in the small molecule pipeline -- fixed by not specifying a protocol, hence allowing the HybridCompatibilityMixin object to automatically handle it. Issue #1039 (PR #1045)
Bug in create_endstates_from_real_systems() -- fixed by setting the global parameters for valence forces to the appropriate endstate. Also added tyk2 transformation test. Issue #1041 (PR #1050).
Bug in the RESTCapableHybridTopologyFactory lifting expression -- fixed by separating the cutoff distance from the lifting distance. (PR #1046)
Fix bug in RelativeFEPSetup that prevents user from controlling the padding when solvating for solvent phase calculations. (PR #1053)
Bug in test_unsampled_endstate_energies_GPU and test_RESTCapableHybridTopologyFactory_energies_GPU -- fixed by removing unit-less rest_radius argument and using default instead. (PR #1057)

Enhancements

Add flag transform_waters_into_ions_for_charge_changes for disabling the introduction of a counterion for charge changing transformations. Issue #1004 (PR #1030)
Perses output yaml file now adds timestamp and ligands names information (for old and new ligands). Issue #998 (PR #1052).
Protein mutation repex internal consistency tests to ensure convergence. So far only testing neutral transformations. Issue #1044 (PR #1054).

Notes

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choderalab/perses-0.10.1.zip md5:f798263f9abe9d4f7d76adc3727b1e54	43.7 MB	Preview Download