AMBER parameter database
The parameters archived here are for use with the AMBER force field and may be freely downloaded. For convenience, the parameter sets are divided into:
- Cofactors
- Carbohydrates
- Proteins
- Lipids (and equilibrated boxes)
- Nucleic acids
- Organic molecules
- Ions
- Solvent boxes
Each parameter set is defined by an OFF or PREP file, a FRCMOD or FRCFLD file and information about the parameters, provided under the name of the contributor, which includes:
- Information about the developers
- A reference to an article where the parameters have been derived and applied
- Additional comments about the parameters e.g. how they were created, what they were used for and known limitations
When using the parameter set, please be sure to cite the given reference. Standard parameters for proteins and nucleic acids are available elsewhere. Finally, please note that we cannot accept responsibility for the parameter quality archived here.
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. A list of links related to AMBER parameters can be found here.
The database is maintained by Richard Bryce, to whom specific correspondence and queries about this site should be directed to:
R.A.Bryce@manchester.ac.uk or by writing to The School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
Cofactors |
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| 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 |
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| monosaccharide units (Glycam04) | PREP | FRCMOD | Woods | |
| monosaccharide units (Glycam04EP, includes lone pairs) | PREP | FRCMOD | Woods | |
| monosaccharide units (Glycam_2000) | PREP | FRCMOD | Woods | |
Lipids |
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| DLPC,DMPC,DPPC,DOPC,POPC,POPE | TGZ | Gould | ||
| DMPC | PREP | FRCMOD | Gould/Rosso | |
| DMPC equilibrated box | PRMTOP | RESTRT | Gould/Rosso | |
| DOPC | PREP | FRCMOD | Gould/Rosso | |
| DOPC equilibrated box | PRMTOP | RESTRT | Gould/Rosso | |
Nucleic Acid |
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| deoxy-5-methylcytosine (dmc) | PREP | FRCMOD | Lankas | |
| deoxy-inosine (di) | PREP | FRCMOD | Lankas | |
| deoxy-2-amino-adenine (daa) | PREP | FRCMOD | Lankas | |
| 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 | |
Proteins |
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| trimethylated lysine (KMe3) | PREP | FRCMOD | Zhang | |
| tert-butyl norleucine (tBuNle) | PREP | FRCMOD | Zhang | |
| neutral analogue of Lys (MeNle) | PREP | FRCMOD | Zhang | |
| trimethyllysine (K3M) | PREP | FRCMOD | Machado | |
| 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 |
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| 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 | |
| duocarmycin SA | OFF | FRCMOD | Case | |
Ions |
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| 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 |
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| 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 |