checking in first stab at minimization script - Githubissues

karanicolaslab / kinasemodeling

Automated pipeline for comparative modeling

MIT License

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checking in first stab at minimization script #3

Open steven-albanese opened 5 years ago

steven-albanese commented 5 years ago

Description

Checking in an initial script for minimizing structures in openMM, per issue #2

Todos

Notable points that this PR has either accomplished or will accomplish.

Fix how files are loaded into the script
pick the proper integrator and solvation model for minimization
calculate score for apo and bound conformations
write test for this script
run over a handful of @pkiruba structures

Questions

What solvent model do we want to use?
What protein/small molecule forcefield should we use?
What type of integrator do we need?
What scoring function should we use? Potential energy? Some sort of interaction energy?

Status

WIP

steven-albanese commented 5 years ago

@jchodera have a few questions on the OpenMM side of things for how to set this up, when you get a chance to look at the script!

steven-albanese commented 5 years ago

What solvent model do we want to use? What protein/small molecule forcefield should we use? What type of integrator/barostat do we need? What scoring function should we use? Potential energy? Some sort of interaction energy?

I imagine that the integrator wouldn't matter since we aren't doing MD, but I'm not sure if we still need to create one for OpenMM as a placeholder