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Bryce Group: Computational Biophysics and Drug Design
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 * AMBER parameter database
 * AMBER parameter database

 * AMBER parameter database
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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

        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




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