SIMLAB DESKTOP MANUAL PRACTICE FILES
Version 0.1.25 documentation, 24 October 2026

Use the manual at https://simlabscience.com/desktop/manual/
This is an extracted subset of the Beyond the Pose companion teaching inputs.
Source structure: RCSB PDB 181L, https://www.rcsb.org/structure/181L

1. Import inputs/181L_protein_only.pdb and inputs/benzene_crystal.sdf through Dock.
2. Follow manual sections 3-8. Box center 26.91,6.13,4.18 Angstrom; side lengths 20 Angstrom; exhaustiveness16;9poses.
3. Build selected pose with AMBER14SB/GAFF2,TIP3P,cubic,1.2nm padding,zero added salt and neutralization.
4. Extract the build ZIP; keep complete run/ tree. Copy these four mdp files into a fresh working copy of run/.
5. Run sections9-13 in Local Lab, checking each stage before continuing.

The MDP set is specific to the stated teaching route. Do not substitute it for a CHARMM protocol.
20ps NVT,50ps NPT,100ps MD demonstrate execution, not research convergence.
Inputs/181L_benzene_reference.pdb is a pose reference, not the protein to build.
No expected binding score is imposed. Keep reports and logs from your own version.
