Supplementary data for Manuscript: Challenges in protein QM/MM simulations with intra-backbone link atoms

Supplementary data for Manuscript: Challenges in protein QM/MM simulations with intra-backbone link atoms

Structure:

Subtilisin
 - pdb-reaction
   - qm-start.pdb      --- A final state of the MM system prior to QM/MM partitioning
   - xtb-rs.pdb        --- GFN2-XTB RS state example
   - xtb-int.pdb       --- GFN2-XTB INT state example
   - xtb-ps.pdb        --- GFN2-XTB PS state example
   - xtb-bb-deprot.pdb --- GFN2-XTB artefact state example
   - dftb-rs.pdb       --- DFTB3 RS state example
   - dftb-int.pdb      --- DFTB3 INT state example
   - dftb-ps.pdb       --- DFTB3 PS state example
   - dftb-anion.pdb    --- DFTB3 artefact state example
 - systems
   - 221-Balanced-None --- CA-C boundary
     - qmmm.top        --- QM/MM topology
     - emqm.gro        --- minimized system
   - 221-Whole-None
   - 221-amber
   - min-Balanced-None --- CB-CA boundary
   - min-While-None
   - min-amber
   - distance-series   --- CA-C boundaries further from the SerOG
     - {resid}.gro     --- minimized system
 - deprotonation.dat --- Plumed file used to perform metadynamics of Ser221 deprotonation
 - reaction.dat      --- Plumed file used to perform metadynamics of acylation reaction
ala-ala
 - metadynamics.dat  --- Plumed file used to perform metadynamics of alanine dipeptide
 - {force field}
   - {charge scheme} --- pme stands for the "Whole" conservation scheme. No pme means "Balanced"
     - {boundary}
       - qmmm.top    --- QM/MM topology
       - emqm.gro    --- minimized system
asnpep
 - metadynamics.dat  --- Plumed file used to perform metadynamics of asparagine model system
 - qmmm.top          --- QM/MM topology of sidechain system
 - emqm.gro          --- minimized system