Minimize structures using openmm

karanicolaslab / kinasemodeling

Automated pipeline for comparative modeling

MIT License

2 stars 1 forks source link

Minimize structures using openmm #2

Open pkiruba opened 5 years ago

pkiruba commented 5 years ago

We should switch to openMM for minimization after structural models have been built.

Need to minimize structures with small molecules bound
Want to score structures with both protein+ligand and protein alone

What solvent model would be best to use for this process?

steven-albanese commented 5 years ago

@jchodera @andrizzi is there an alternative to gaffTemplateGenerator in openmoltools for loading in small molecules to OpenMM with gaff? We're just looking to minimize protein::ligand structures at the moment.

edit: We're looking to avoid using an openeye license here!