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README.md

Martini 3 small-molecule database - Models

The file martini_v3.0.0_small_molecules_v1.itp contains the up-to-date collection of Martini 3 small molecule models.

One way to look for a particular molecule is to search that file for the molecule common name in capital letters, e.g., BENZENE, TOLUENE, etc. Alternatively, the folder SMILES/ contains the SMILES string of the molecules for which a Martini 3 model exists. You can also see the list of unique identifies (uIDs), names, and SMILES strings in table-sm3-SI.tex.

Description of available files

For a given molecule with unique string ID MOL, 8 files are available:

  1. MOL.smiles: the SMILES string represting the molecule (folder SMILES/);

  2. MOL.itp: the Martini 3 topology file in GROMACS format (folder itps/opt-????/);

  3. MOL.gro: the Martini 3 coordinate file in GROMACS format (folder gros/);

  4. MOL_LigParGen.pdb: atomistic structure as obtained from the LigParGen server by entering the corresponding SMILES string; (folder AA/oplsaa-LigParGen/);

  5. MOL_LigParGen.itp: OPLS-AA/1.14*CM1A-LBCC topology file (in GROMACS format) as obtained from the LigParGen server by entering the corresponding SMILES string; (folder AA/oplsaa-LigParGen/);

  6. MOL_oplsaaTOcg_\*.ndx: the AA-to-CG index file (folder mapping-cgbuilder/oplsaa-LigParGen/MOL);

  7. MOL_cgTOoplsaa_\*.map: the CG-to-AA mapping file (folder mapping-cgbuilder/oplsaa-LigParGen/MOL);

  8. MOL_LigParGen_cgbuilder.png: a screenshot to visualize the beads and underlying atomistic structure (folder mapping-cgbuilder/oplsaa-LigParGen/MOL);