Iván Pulido
Iván Pulido
From the `perses` side of things we noted a discrepancy when analyzing the Nonbonded forces in our test systems. Original issue in perses: https://github.com/choderalab/perses/pull/1124 A table summarizing it is as...
Instead of forcing the perses `AtomMapper`, we should allow users to specify mapping dictionaries that could be created with external tools in our pipelines. This is related to https://github.com/choderalab/perses/issues/1204
Since the RCSB is officially dropping support for PDB files in favor of using PDBx/mmcif formatted files, I think we should consider making sure we support this format. I suspect...
From https://github.com/choderalab/openmmtools/pull/544#issuecomment-1071113024 We need to double check how imaging of complex is handled.
## Description Adds handling of max temperature parameter from input yaml file with CLI. ## Motivation and context We need to be able to specify the maximum temperature from input...
As part of our big refactor we are planning on using [`gufe`](https://github.com/OpenFreeEnergy/gufe) objects as base objects for most of the things we do. Writing a protein mutation protocol for [`alchemiscale`](https://github.com/openforcefield/alchemiscale)...
Currently perses REST capabilities are not being used in the small molecule pipeline from CLI. One quick way to do this is passing a configuration option from the YAML file...
While trying to run the new edges in the https://github.com/openforcefield/protein-ligand-benchmark/tree/new-perses-edges dataset I noticed that at least one edge is failing when creating the mapping with the following error: ```python ---------------------------------------------------------------------------...
We want to write the PDBs for the initial and final states of the simulation in the subdirectory where the openmm systems live (XML subdir).
We should be able to integrate other atom mappers such as the TimeMachine mapper or similar, that we could use in perses for doing the mapping.