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 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

       
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

       
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
OFF FRCFLD Stuchebrukhov

Proteins

       
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

       
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