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, nucleic acids, organic molecules and counter/metal ions. 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; and 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 (Cornell et al 1995) 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. Guidelines are available for AMBER parameter development. 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
flavin mononucleotide (fully oxidized), FMN OFF FRCFLD Suhnel
flavin adenine dinucleotide anion, FADH(-) OFF FRCFLD Stuchebrukhov
heme (all-atom) PREP FRCMOD Giammona
heme (united-atom) PREP FRCMOD Giammona

Carbohydrates
2-[alpha-D-manno-] non-terminal PREP FRCMOD Woods
3,4,6-[beta-D-manno-] branched PREP FRCMOD Woods
3,4-[2-acetamido-beta-D-gluco-] branch (N-linkages) PREP FRCMOD Woods
4-[2-acetamido-beta-D-gluco-] non-terminal (O-linkages) PREP FRCMOD Woods
3,6-[alpha-D-manno-] branch PREP FRCMOD Woods
3,6-[beta-D-manno-] branch PREP FRCMOD Woods
3-[beta-D-galacto-] non-terminal PREP FRCMOD Woods
3-[alpha-D-galNAc-] non-terminal PREP FRCMOD Woods
3-[alpha-D-manno-] non-terminal PREP FRCMOD Woods
3-[beta-D-manno-] non-terminal PREP FRCMOD Woods
3-[2-acetamido-beta-D-gluco-] non-terminal (O-linkages) PREP FRCMOD Woods
4,6-[2-acetamido-beta-D-gluco-] branch (N-linkages) PREP FRCMOD Woods
4,6-[2-acetamido-beta-D-gluco-] non-terminal (O-linkages) PREP FRCMOD Woods
4-[2-acetamido-beta-D-gluco-] non-terminal (N-linkages) PREP FRCMOD Woods
4-[2-acetamido-beta-D-gluco-] non-terminal (O-linkages) PREP FRCMOD Woods
6-[alpha-D-manno] non-terminal PREP FRCMOD Woods
6-[beta-D-manno-] non-terminal PREP FRCMOD Woods
6-[2-acetamido-beta-D-gluco]- non-terminal (O-linkages) PREP FRCMOD Woods
alpha-(axial)-L-fuco- terminal PREP FRCMOD Woods
alpha-D-galacto- terminal PREP FRCMOD Woods
beta-D-galacto- terminal PREP FRCMOD Woods
alpha-D-manno- terminal PREP FRCMOD Woods
B-D-manno- terminal PREP FRCMOD Woods
2-acetamido-beta-D-gluco- terminal (N-linkages) PREP FRCMOD Woods
2-acetamido-beta-D-gluco- terminal (O-linkages) PREP FRCMOD Woods
O-methyl aglycon PREP FRCMOD Woods

Proteins

Nucleic Acid
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

Organic Molecules

Counter/Metal Ions
manganese(2+) PREP FRCMOD Bradbrook
calcium(2+) PREP FRCMOD Bradbrook

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Last modified Mon Jan 7 21:49:22 GMT 2002