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Add apo ACE2 and SARS RBD:ACE2 structures #31

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12 changes: 12 additions & 0 deletions system-preparation/2ajf_ace2/README.md
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## SARS-CoV ACE2

### Source structures from the [protein databank](http://rcsb.org):
* 2AJF - SARS coronavirus spike receptor-binding domain (RBD) complexed with ACE2 (2.9 angstrom, X-ray diffraction)

### Folding@home input file preparation
1. Extract ACE2 chain from 2AJF.
2. Protonate and cap using Schrodinger's Maestro
3. Prepare system and equilibrate using OpenMM:
- Solvate, minimize, and equilibrate for 5ns, at 2fs timestep, 4amu hydrogens with `simulate_2ajf_ace2.py`
4. Equilibrate at longer time step using OpenMM:
- Starting from the above equilibrated snapshots, equilibrate further for 1.25ns, at 4fs timestep, 4amu hydrogens with `simulate_4amu_4fs.py`
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