Ligand Database in NAFlex (Amber Parameters)
Useful links to ligand parameters and modified nucleic acids parameters (Amber format):
- AMBER parameter database (Richard Bryce - Manchester)
- Modified Nucleic Acid Parameters Database (John SantaLucia - Wayne)
List of Ligand parameters of MoDEL library, included in NAFlex (click on a ligand name to obtain more information):
- MoDEL Ligand Library
| 1DA | 1MA | 1MG | 2MG | 2PH | 2PR | 4HA | 5GP | 5MC | 5MU |
| 7MG | 8OG | 998 | A80 | ABC | ACM | ACN | ACT | ACY | ADE |
| ADN | ADP | AHA | APF | ARN | ATP | AZI | B18 | BDN | BGL |
| BHP | BMA | BME | BML | BNZ | BOG | BU1 | Br- | CA2 | CBI |
| CHX | CIT | CMO | CO3 | COT | CYH | CYN | Ca2 | Cd2 | Co2 |
| Cs+ | Cu2 | DCM | DDQ | DGG | DIO | DM | DMF | DMS | DNC |
| DOX | DTT | EDO | EHN | EOH | EPE | F10 | FMN | Fe2 | GDP |
| GLA | GLB | GOL | H2U | HEM | IDA | IMD | IND | INT | IOL |
| IPA | IPH | K+ | KDG | LDA | LYN | LYS | Li+ | M2G | MAN |
| MEE | MES | MG2 | MOH | MPD | MR9 | MSM | MTX | Mg2 | Mn2 |
| NAD | NEO | NH3 | NH4 | NO3 | Na+ | Ni2 | OAA | OMC | OMG |
| OXL | OXY | PBP | PEG | PGA | PLM | PO2 | POP | PP7 | PPI |
| PPV | PSU | PYD | RGUA | RIP | RRT | RTL | S6G | S6G3 | S6G5 |
| SAM | SB2 | SBI | SDG | SIN | SKD | SO4 | SOA | SPM | SUL |
| TAR | TCD | THM | TNL | TRS | TTD | TYM | URA | URE | V25 |
| WAT | YG | Zn2 | apf | arg | gly | lys | sHBO | tRNA | thioG_TG |
