search

OpenFreeEnergy / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
MIT License
13 stars 1 forks source link

Allow for partial charge method setting specification #47

Closed ijpulidos closed 1 month ago

ijpulidos commented 3 months ago

It is convenient for users to be able to specify the partial charge generation method, especially if other toolkits different from ambertools (such as OpenEye) are available. Using the OpenFFPartialChargeSettings model from openfe seems like the way to go.

ijpulidos commented 3 months ago

This is related to the comment in https://github.com/choderalab/feflow/pull/38#issuecomment-2147979007 @dotsdl

dotsdl commented 3 months ago

Thanks @ijpulidos, I will take this one on!

dotsdl commented 3 months ago

Actually, @ianmkenney: is this something you would be willing to hit?

IAlibay commented 3 months ago

Just a brief outline of what needs doing.

  1. Re-create this (I can't remmber if we aligned on the off_small_mols dictionary yet): https://github.com/OpenFreeEnergy/openfe/blob/48dcbb26e894c98566731b65224465c25a3c0fe4/openfe/protocols/openmm_rfe/equil_rfe_methods.py#L621-L647
  2. Change this loop: https://github.com/choderalab/feflow/blob/e7fb6f67bd198c39a0abaa41bd700da778dea8b3/feflow/protocols/nonequilibrium_cycling.py#L197-L210 a. Instead it should be a call to the charge assignment method and then after that a loop over molecules passing them to system_generator.create_system
ijpulidos commented 1 month ago

Solved by #49