Please consider contributing your AMBER parameters to this database for other AMBER users to download and use, and to provide a starting point for parametrization of similar molecules. Guidelines are available for AMBER parameter development (AMBER9 Manual, "Specifying a force field", or AMBER8 Manual, "Science Background", p.254). A list of links related to AMBER parameters is also maintained. The database is maintained by Richard Bryce, to whom specific correspondence and queries about this site should be directed, by email or by writing to The School of Pharmacy & Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
Cofactors | ||||
| GDP (revised phosphate parameters) | PREP | FRCMOD | Carlson | |
| GTP (revised phosphate parameters) | PREP | FRCMOD | Carlson | |
| ADP (revised phosphate parameters) | PREP | FRCMOD | Carlson | |
| ATP (revised phosphate parameters) | PREP | FRCMOD | Carlson | |
| flavin mononucleotide (fully oxidized), FMN | OFF | FRCFLD | Suhnel | |
| flavin adenine dinucleotide anion, FADH(-) | OFF | FRCFLD | Stuchebrukhov | |
| NAD(+) | OFF | FRCMOD | Walker | |
| NADH | OFF | FRCMOD | Walker | |
| NAD(+) | PREP | FRCMOD | Ryde | |
| NADH | PREP | FRCMOD | Ryde | |
| NADP(+) | PREP | FRCMOD | Ryde | |
| NADPH | PREP | FRCMOD | Ryde | |
| NADP(+) | PREP | FRCMOD | Gready | |
| NADPH | PREP | FRCMOD | Gready | |
| heme (all-atom) | PREP | FRCMOD | Giammona | |
| heme (united-atom) | PREP | FRCMOD | Giammona | |
Carbohydrates | ||||
| monosaccharide units (Glycam04) | PREP | FRCMOD | Woods | |
| monosaccharide units (Glycam04EP, includes lone pairs) | PREP | FRCMOD | Woods | |
| monosaccharide units (Glycam_2000) | PREP | FRCMOD | Woods | |
Nucleic Acid | ||||
| 8-oxoguanine | PREP | FRCMOD | Simmerling | |
| modified bases appearing in tRNA-phe from yeast | OFF | FRCMOD | Case | |
| 2-(2'-hydroxyphenyl)benzoxazole/sugar (modified DNA nucleotide) | OFF | FRCMOD | Case | |
| 2-amino purine | OFF | FRCMOD | Case | |
| R-guanosine of GDP-mannose | PREP | FRCMOD | Imberty | |
| pyrophosphate of GDP-mannose | PREP | FRCMOD | Imberty | |
| mannose of GDP-mannose | PREP | FRCMOD | Imberty | |
| 3' phosphoramidate modified DNA/RNA | PREP | FRCMOD | Cieplak | |
| thymine dimer | OFF | FRCFLD | Stuchebrukhov | |
Proteinstrimethylated lysine ( KMe3), tert-butyl norleucine (tBuNle), and the neutral analogue of Lys (MeNle) | ||||
| trimethylated lysine (KMe3) | PREP | FRCMOD | Zhang | |
| tert-butyl norleucine (tBuNle) | OFF | FRCMOD | Zhang | |
| neutral analogue of Lys (MeNle) | OFF | FRCMOD | Zhang | |
| 5,5,5-trifluoroleucine | OFF | FRCMOD | Pendley | |
| 5,5,5,5',5',5'-hexafluoroleucine | OFF | FRCMOD | Pendley | |
| N-terminal ornithine | OFF | FRCMOD | Pendley | |
| ornithine | OFF | FRCMOD | Pendley | |
| heptanoic acid | OFF | FRCMOD | Pendley | |
| phosphohistidine with single protonated phosphate group, phosphorylated at ND1, HIS(ND1)-PO2(OH) | OFF | FRCMOD | Sticht | |
| phosphohistidine with unprotonated phosphate group, phosphorylated at ND1, HIS(ND1)-PO3 | OFF | FRCMOD | Sticht | |
| phosphohistidine with single protonated phosphate group, phosphorylated at NE2, HIS(NE2)-PO2(OH) | OFF | FRCMOD | Sticht | |
| phosphohistidine with unprotonated phosphate group, phosphorylated at NE2, HIS(NE2)-PO3 | OFF | FRCMOD | Sticht | |
| phosphoserine with single protonated phosphate group, SER-PO2(OH) | OFF | FRCMOD | Sticht | |
| phosphoserine with unprotonated phosphate group, SER-PO3 | OFF | FRCMOD | Sticht | |
| phosphothreonine with single protonated phosphate group, THR-PO2(OH) | OFF | FRCMOD | Sticht | |
| phosphothreonine with unprotonated phosphate group, THR-PO3 | OFF | FRCMOD | Sticht | |
| phosphotyrosine with single protonated phosphate group, TYR-PO2(OH) | OFF | FRCMOD | Sticht | |
| phosphotyrosine with unprotonated phosphate group, TYR-PO3 | OFF | FRCMOD | Sticht | |
| phosphoserine | OFF | FRCMOD | Craft | |
| phosphothreonine | OFF | FRCMOD | Craft | |
| phosphotyrosine | OFF | FRCMOD | Craft | |
Organic Molecules | ||||
| poly(1-vinylpyrrolidin-2-one) (PVP monomer) | OFF | FRCMOD | Contini | |
| poly(1-vinylpyrrolidin-2-one) (PVP monomer) | OFF | FRCMOD | Contini | |
| poly(1-vinylpyrrolidin-2-one) (PVP monomer) | OFF | FRCMOD | Contini | |
| poly(1-vinylpyrrolidin-2-one) (PVP monomer) | OFF | FRCMOD | Contini | |
| poly(1-vinylpyrrolidin-2-one) (PVP monomer) | OFF | FRCMOD | Contini | |
| saquinavir | PREP | FRCMOD | Lepsik | |
| indinavir | PREP | FRCMOD | Lepsik | |
| calix[4]pyrrole | OFF | FRCMOD | Blas | |
| octafluorocalix[4]pyrrole | OFF | FRCMOD | Blas | |
| tri-n-butyl-phosphate | PREP | FRCMOD | Baaden | |
| calix[4]arenes | PREP | FRCMOD | Baaden | |
| calicheamyicin | OFF | FRCMOD | Case | |
| duocarmycin SA | OFF | FRCMOD | Case | |
Ions | ||||
| Mg(2+) | PREP | FRCMOD | Sorensen | |
| cobalt hexaammine | OFF | FRCMOD | Cheatham | |
| hydronium ion, H3O(+) | PREP | FRCMOD | Baaden | |
| nitrate/nitric acid, NO3(-)/HNO3 | PREP | FRCMOD | Baaden | |
| triflate, CF3SO3(-) | PREP | FRCMOD | Baaden | |
| perchlorate, ClO4(-) | PREP | FRCMOD | Baaden | |
| lanthanides, Eu(3+), La(3+), Yb(3+) | PREP | FRCMOD | Baaden | |
| Mn(2+) | PREP | FRCMOD | Bradbrook | |
| Ca(2+) | PREP | FRCMOD | Bradbrook | |
Solvent boxes | ||||
| dimethylsulfoxide, DMSO (all atom) | BOX | OFF | FRCMOD | Dalmaris |
| acetonitrile, CH3CN (all atom) | BOX | PREP | FRCMOD | Jaime |
| acetonitrile, CH3CN (united atom) | BOX | OFF | FRCMOD | Blas |
| dichloromethane, CH2Cl2 (united atom) | BOX | OFF | FRCMOD | Blas |
| methanol | BOX | PREP | FRCMOD | Caldwell |
| chloroform, CHCl3 | BOX | PREP | FRCMOD | Caldwell |
| N-methyl acetamide | BOX | PREP | FRCMOD | Caldwell |