This is a collection of topology and parameter files generated for 264 ligands by parameter assignment programs. The investigated parameter assignment programs and generalized force fields are tabulated below:
| Parameter Assignment Program | Charge Model | Force Field | Parameter Set |
|---|---|---|---|
| CGenFF v 2.5.1 | N/A | CGenFF v4.6 | CGenFF |
| CGenFF legacy v 1.0 | N/A | CGenFFv3.0.1 | CGenFF Legacy |
| MATCH v 0.01 | N/A | CGenFFv3.0.1 | MATCH/CGenFF |
| Antechamber, AmberTools21 | RESP | GAFF2.11 | GAFF2/RESP |
| Antechamber, AmberTools21 | AM1-BCC | GAFF2.11 | GAFF2/AM1-BCC |
| Antechamber, AmberTools21 | AM1-BCC | GAFF1.81 | GAFF/AM1-BCC |
In addition to the parameter sets above, we investigated the modified CGenFFv3.0.1, modified GAFF2.11, and OpenFF 1.2.0 Parsley topologies and parameters provided by Gapsys et al, J. Chem. Inf. Model. 2022.
Data pertaining to Gasys et al are provided in the respective GitHub repository.
├── cgenff
│ ├── ligand_id
│ │ ├── mol.str (CGenFF stream file output)
├── cgenff_legacy
│ ├── ligand_name
│ │ ├── mol.str (CGenFF Legacy stream file output)
├── match_cgenff
│ ├── ligand_id
│ │ ├── mol.rtf (MATCH topology file output)
│ │ ├── mol.prm (MATCH parameter file output)
│ │ ├── mol.log (MATCH log output)
├── gaff_am1_bcc
│ ├── ligand_id
│ │ ├── mol_am1bcc_gaff.ac (Antechamber topology file output)
│ │ ├── mol_gaff.frcmod (Antechamber parameter file output)
├── gaff2_am1_bcc
│ ├── ligand_id
│ │ ├── mol_am1bcc_gaff2.ac (Antechamber topology file output)
│ │ ├── mol_gaff2.frcmod (Antechamber parameter file output)
├── gaff2_resp
│ ├── ligand_id
│ │ ├── resp_charges.txt (RESP charges)
└── └── └── mol_gaff2.frcmod (Antechamber parameter file output)
Ligand IDs are based on the naming provided in Gapsys et al, J. Chem. Inf. Model. 2022, which include the protein system the ligands are associated with followed by their ligand name.
RESP charges were calculated through Psi4 and workflows developed in Kumar et al, J. Chem. Theory Comput. 2022.
Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell Jr. Preserving the Integrity of Empirical Force Fields. Under Review.