AMBER parameter database
The parameters archived here are for use with the AMBER force field and may be freely downloaded.
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 external 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 (ie. the published source article where the parameters were derived and applied). 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 Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
Cofactors
Mo(IV)/water | PREP | FRCMOD | Szaleniec |
Molybdopterin guanine dinucleotide (distal to FeS cluster) | PREP | FRCMOD | Szaleniec |
Molybdopterin guanine dinucleotide (near FeS cluster) | PREP | FRCMOD | Szaleniec |
Cys (-Mo(IV)) | PREP | FRCMOD | Szaleniec |
Cys (-Fe1 of Fe4S4) | PREP | FRCMOD | Swart/Szaleniec |
Cys (-Fe2 of Fe4S4) | PREP | FRCMOD | Swart/Szaleniec |
Cys (-Fe3 of Fe4S4) | PREP | FRCMOD | Swart/Szaleniec |
Cys (-Fe4 of Fe4S4) | PREP | FRCMOD | Swart/Szaleniec |
Fe4S4 cluster | PREP | FRCMOD | Swart/Szaleniec |
9-cis retinal | PREP | FRCMOD | Church |
11-cis retinal | PREP | FRCMOD | Church |
BVQ (norpseudo-B12) | OFF | FRCMOD | Ren |
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 |
Lipids
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
L-ribonucleotides (for AmberTools14 and 16) | ZIP (AT14) | ZIP (AT16) | Dudek/Trylska |
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 |
Proteins
cysteine modified by malondialdehyde (MDA) | PREP | FRCMOD | Mendez-Cuadro |
cysteine modified by 4-hydroxy-2-hexenal (HHE) | PREP | FRCMOD | Mendez-Cuadro |
cysteine modified by 4-oxo-2-nonenal (ONE) | PREP | FRCMOD | Mendez-Cuadro |
7-azatryptophan (TRN) | MOL2 | FRCMOD | Lepsik |
7-fluorotryptophan (TRF) | MOL2 | FRCMOD | Lepsik |
scaled charge aspartate (ASS) | OFF | FRCMOD | Lepsik |
scaled charge glutamate (GLS) | OFF | FRCMOD | Lepsik |
scaled charge C-terminal glycine (CGS) | OFF | FRCMOD | Lepsik |
arginine modified by 4-hydroxy-2-nonenal (4-HNE) | OFF | FRCMOD | Mendez-Cuadro |
cysteine modified by 4-hydroxy-2-nonenal (4-HNE) | PREP | FRCMOD | Mendez-Cuadro |
histidine modified by 4-hydroxy-2-nonenal (4-HNE) | OFF | FRCMOD | Mendez-Cuadro |
lysine modified by 4-hydroxy-2-nonenal (4-HNE) | PREP | FRCMOD | Mendez-Cuadro |
zwitterionic amino acids | OFF | FRCMOD | Horn |
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
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
scaled charge calcium (CA) | OFF | FRCMOD | Lepsik |
scaled charge chloride (CL) | OFF | FRCMOD | Lepsik |
scaled charge potassium (K) | OFF | FRCMOD | Lepsik |
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 |