AMBER Atom Types (parm94.dat)

Note that this is a purely all-atom force field.

• CT: any sp3 (four explicit substituents).

• C : any sp2 carbonyl carbon
• C*: sp2 aromatic carbon in a five-membered ring next to two carbons (e.g. C_gamma in tryptophan).
• CA: any sp2 aromatic carbon and C_epsilon of Arg.
• CB: sp2 aromatic at junction of five- and six-membered rings (e.g. C_delta in tryptophan and C4 and C5 in purines Ade & Gua).
• CC: sp2 aromatic in a five-membered ring with one substituent and next to a nitrogen (e.g. C_gamma in histidine).
• CK: sp2 aromatic in a five-membered ring, between two nitrogens and bonded to one explicit hydrogen (C8 in purines).
• CM: sp2 carbon, more double bonded character than benzene.
• CN: sp2 aromatic junction between five- and six-membered rings and bonded to C-R and N-R (e.g. C_epsilon in Trp).
• CQ: sp2 in six-membered ring between two lone pair nitrogens (e.g. C2 in purines).
• CR: sp2 aromatic in a five-membered ring between two nitrogens (e.g. C_epsilon in histidine).
• CV: sp2 aromatic in a five-membered ring next to a carbon and a lone pair nitrogen (e.g. C_delta in His(delta)).
• CW: sp2 aromatic in a five-membered ring next to a carbon and NH (e.g. C_delta in His(epsilon) and in Trp).

• N3: any sp3 (four substituents; e.g. lysine-Nzeta).

• N : sp2 in amides.
• N*: sp2 in five- or six-membered ring with substituent (e.g. N9 in purines, N1 in pyrimidines).
• N2: sp2 in amines (e.g. nucleic acids, Arg, and guanidium ions).
• NA: sp2 in aromatic rings with attached hydrogen (e.g. Gua, Trp, protonated His).
• NB: sp2 in five-membered ring with lone pair (e.g. N7 in purines).
• NC: sp2 in six-membered ring with lone pair (e.g. N3 in purines).

• OW: oxygen in TIP3P water model.
• OH: alcohols, tyrosine, and protonated carboxylic acids.
• OS: ethers and esters.

• O : carbonyl.
• O2: anionic acids (e.g. carboxyl and phosphate).

• P : phosphorus in phosphate groups.
• S : sulfurs in disulfide linkages.
• SH: sulfur in cysteine.
• LP: lone pairs.

• H : attached to N.
• HO: in alchohols and acids.
• HW: in TIP3P water model.
• HS: attached to sulfur.
• HA: attached to aromatic carbon.
• HC: attached to aliphatic carbon with no electron-withdrawing substituents.
• H1: attached to aliphatic carbon with one electron-withdrawing substituent.
• H2: attached to aliphatic carbon with two electron-withdrawing substituents.
• H3: attached to aliphatic carbon with three electron-withdrawing substituents.
• HP: attached to carbon directly bonded to formally positive atoms (e.g. C next to NH3+ of Lys).
• H4: attached to aromatic carbon with one electronegative neighbor (e.g. C5 of Trp, C6 of Thy).
• H5: attached to aromatic carbon with two electronegative neighbors (e.g. H8 of Ade and Gua and H2 of Ade).