This is the example calculation for psilocin CCS calculation. The directory is organized as follows:
- The directory is named after an identifier. In this case, the Human Metabolome Database ID for psilocin
- The charge of the adducts (-2, -1, 1)
- charged_model.smi contains possible (de)protonation isomers, referred to as models
- The other directories are all calculation results used in the workflow (‘site_screen’, ‘generated_conformers’, etc). They are organized by each model.
- The final results are inside the ensemble directory, titled results.csv
The results directories are organized as follows:
Identifier
- Charge of adduct
- charged_model.smi : smiles of charge models
- model.smi : smiles of hypothesized charge models ((de) protonation isomer)
- site_screen : single point energy calculation of ionized metabolites
- generated_conformers : <= 1000 conformers generated from SMILES
- optimized_conformers : conformers refined by ANI-2x potential
- clustered_conformers : conformers clustered by AutoGraph
- ensemble : calculation pertaining to the modeled conformational ensemble
Each result directories (generated_conformers, optimized_conformers, clustered_conformers, and ensemble) are organized by the charged model considered
Ensemble
- modelX
- i.in : QUICK input file for geometry optimization/charge calculation
- i.out : QUICK output file for geometry optimization/charge calculation
- i.pqr : geometry optimization/charge calculation results in PQR format
- i.hpccs : HPCCS calculation result
- energy.csv : optimized energy values
- results.csv : conformer-wise CCS values
- ccs.txt : ensemble averaged CCS value with absolute and relative calculated error