List of supported particles

Haddock3 supports (i.e., can process automatically including topology generation, rebuilding of the missing atoms, and point mutations) various carbohydrates, ions, co-factors and a plethora of the modified amino acids - you can check a complete list below.

Supported carbohydrates

• A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4
• ABE: alpha-D-Abequopyranose
• BDP: beta-D-glucoronic acid
• BGC: beta-D-glucopyranose
• BMA: beta-D-mannopyronose
• FCA: alpha-D-fucopyranose
• FCB: beta-D-fucopyranose
• FUC: alpha-L-fucopyranose
• FUL: beta-L-fucopyranose
• GAL (GLB): beta-D-galactopyranose
• GLA: alpha-D-galactopyranose
• GLC: alpha-D-glucopyranose
• GCS: 2-N-beta-D-glucopyranose (glucosamine)
• GXL: alpha-L-galactopyranose
• MAG: 2-N-Acetyl-beta-D-glucopyranose + Methyl at O1
• MAN: alpha-D-mannopyranose
• MMA: methyl alpha-D-mannopyranoside
• NAA: 1-O-methyl-2-N-Acetyl-alpha-D-glucopyranose
• NAG: 2-N-acetyl-beta-D-glucopyranose
• NAM: 1-O-methyl-2-N-Acetyl-beta-D-glucopyranose
• NDG: 2-N-acetyl-alpha-D-glucopyranose
• NGA: 2-N-acetyl-beta-D-galactopyranose
• NGM: 1-O-methyl-2-N-Acetyl-alpha-D-galactopyranose
• RAM: alpha-L-rhampyranose
• SIA: alpha-N-acetyl neuraminic acid
• SIB: beta-N-acetyl neuraminic acid
• XYP: beta-D-xylopyranose
• XYS: alpha-D-xylopyranose

Carbohydrates should be provided with record HETAM, e.g.:

HETATM    9  C1  NAG B 102     171.992  99.750 236.168  1.00 10.00           C

Supported ions

Ions should be provided with their charge and a HETAM flag. Residue name should contain the absolute charge (e.g. ZN2) while atom name should have the exact charge (e.g. ZN+2), e.g.:

HETATM 3833 ZN+2 ZN2 A  42      21.391  -8.794  33.944  1.00 24.37          ZN  

Supported multi-atom ions

• PO4: Phosphate
• SO4: Sulphate
• WO4: Tungstate

Supported water molecules

• TIP/WAT: water molecule with as atoms OH2,H1,H2

Supported co-factors

The following co-factors are defined using HADDOCK's internal parameters:

• HEB: Heme B, open pdb example
• HEC: Heme C, open pdb example

Co-factors should be provided with record HETAM, e.g.:

HETATM    1  FE  HEB   500       3.565   0.487   0.949  1.00 15.00          

For the other co-factors, HADDOCK3 will try to generate the topology and parameters automatically, using the PRODRG server - do add autotoppar = true to the [topoaa] to enable this option. If the co-factor is not available in PRODRG, you will have to generate and provide the topology and parameters yourself.

Supported nucleic acid bases

Supported modified amino acids

All supported modified amino acids are in this list and must be defined as ATOM.

• ACE: N-terminal acetyl group.

  Atoms: CA,HA1,HA2,HA3,C,O

• ALY: Acetylated LYS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2,NZ,HZ1,CZ,OZ,CM,HM1,HM2,HM3,C,O

• ASH: protonated ASP.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,OD1,OD2,HD2,C,O

• CFE: CYS with an iron sulfur cluster. HADDOCK will automatically search for closeby CYF residues and created bonds with the iron cluster.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,SG,FE1,SF1,FE2,SF2,C,O

• CSP: phosphorylated CYS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,SG,P,O1P,O2P,O3P,C,O

• CTN: C-terminal amide group.

  Atoms: N,H1,H2

• CYC: special for covalent docking - vdw of Sulphur reduced.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,SG,C,O

• CYF: CYS without the sulfur H (for coordinating metals).

  Atoms: N,HN,CA,HA,CB,HB1,HB2,SG,C,O

• CYM: CYS with MTSL grouped.

  Atoms: CAC,CAS,CAD,NAQ,OAH,HAA,CAR,CAA,CAB,CAI,CAO,CAJ,SAL,N,HN,CA,HA,CB,HB1,HB2,SG,C,O

• DDZ: 3,3,-dihydroxy ALA.

  Atoms: N,HN,CA,HA,CB,HB1,OG1,HG1,OG2,HG2

• GLH: protonated GLU.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,OE1,OE2,HE2,C,O

• HY3: 3-hydroxyproline.

  Atoms: N,CA,HA,CB,OB1,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,C,O

• HYP: 4R-hydroxyproline.

  Atoms: N,CA,HA,CB,HB1,HB2,CG,OG1,HG1,HG2,CD,HD1,HD2,C,O

• M3L: trimethyl LYS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2,NZ,HZ1,HZ2,CM1,HM11,HM12,HM13,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O

• MLY: dimethyl LYS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2,NZ,HZ1,HZ2,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O

• MLZ: monomethyl LYS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2,NZ,HZ1,HZ2,CM3,HM31,HM32,HM33,C,O

• MSE: Selenomethionine.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,SE,CE,HE1,HE2,HE3,C,O

• NEP: NE phosphorylated HIS.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,ND1,HD1,CD2,HD2,CE1,HE1,NE2,P,O1P,O2P,O3P,C,O

• NME: C-terminal N-Methyl.

  Atoms: N,HN,CA,HA1,HA2,HA3

• PNS: Phosphopanthetine Serine.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,OG,P,O1P,O2P,O3P,C,O,C28,H28,H29,C29,C30,H31,H32,H30,C31,H34,H35,H33,C32,H36,O33,H46,C34,O35,N36,H48,C37,H37,H38,C38,H39,H4A,C39,O40,N41,H41,C42,H42,H43,C43,H44,H45,S44,H47

• PTR: O-Phosphotyrosine.

  Atoms: N,CA,C,O,OXT,CB,CG,CD1,CD2,CE1,CE2,CZ,OH,P,O1P,O2P,O3P,1HN,2HN,HA,HXT,1HB,2HB,HD1,HD2,HE1,HE2,PHO2,PHO3

• SEC: Serine with reduced vdw on the OG oxygen for covalent docking.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,OG,C,O

• SEP: phosphorylated SER.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,OG,P,O1P,O2P,O3P,C,O

• TOP: phosphorylated THR.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,OG,P,O1P,O2P,O3P,CG2,HG21,HG22,HG23,C,O

• TYP or PTR: phosphorylated TYR.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH,P,O1P,O2P,O3P,C,O

• TYS: sulfonated TYR.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH,S,O1S,O2S,O3S,C,O

• QSR: serotonylated GLN.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,OE1,NE2,HE2,CSA,HSA1,HSA2,CSB,HSB1,HSB2,HSE1,NSE1,CSD1,HSD1,CSG,CSD2,CSE2,CSE3,HSE3,CSZ3,OSZ3,HSZ3,CSH2,HSH2,CSZ2,HSZ2,C,O,

• PCA: pyro-glutamic acid.

  Atoms: N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,OE,C,O