AMBER has specific atom names to describe the environment (and associated bonding) of that atom. Atom typing is not found in the PDB, but it is found in anything dealing with a force field (specifically prepi and frcmod files). The traditional AMBER force field atom types can be found here and a description of the terms themselves can be found on the Cerius2 site. The following are the atom types in GAFF, or the General AMBER Force Field, taken from the AMBER website.
Table: Amber Atom Types in General AMBER Force Field (GAFF)
| Atom Name | Description | Category |
|---|---|---|
| c | sp2 C in C=O, C=S | basic |
| c1 | sp1 C | basic |
| c2 | sp2 C, aliphatic | basic |
| c3 | sp3 C | basic |
| ca | sp2 C, aromatic | basic |
| n | sp2 N in amide | basic |
| n1 | sp1 N | basic |
| n2 | sp2 N with 2 substituted double bond | basic |
| n3 | sp3 N with 3 substituted | basic |
| n4 | sp3 N with 4 substituted | basic |
| na | sp2 N with 3 substituted | basic |
| nh | amine N connected to the aromatic rings | basic |
| no | N in nitro group | basic |
| o | sp2 O in C=O, COO- | basic |
| oh | sp3 O in hydroxyl group | basic |
| os | sp3 O in ether and ester | basic |
| s2 | sp2 S (p=S, C=S etc) | basic |
| sh | sp3 S in thiol group | basic |
| ss | sp3 S in -SR and SS | basic |
| s4 | hypervalent S, 3 substituted | basic |
| s6 | hypervalent S, 4 substituted | basic |
| hc | H on aliphatic C | basic |
| ha | H on aromatic C | basic |
| hn | H on N | basic |
| ho | H on O | basic |
| hs | H on S | basic |
| hp | H on P | basic |
| p2 | sp2 P (C=P etc) | basic |
| p3 | sp3 P, 3 substituted | basic |
| p4 | hypervalent P, 3 substituted | basic |
| p5 | hypervalent P, 4 substituted | basic |
| f | any F | basic |
| cl | any Cl | basic |
| br | any Br | basic |
| i | any I | basic |
| h1 | H on aliphatic C with 1 electron-withdrawing group | special |
| h2 | H on aliphatic C with 2 electron-withdrawing groups | special |
| h3 | H on aliphatic C with 3 electron-withdrawing groups | special |
| h4 | H on aliphatic C with 4 electron-withdrawing groups | special |
| h5 | H on aliphatic C with 5 electron-withdrawing groups | special |
| cc(cd) | inner sp2 C in conjugated ring systems | special |
| ce(cf) | inner sp2 C in conjugated chain systems | special |
| cp(cq) | bridge aromatic C | special |
| cu | sp2 C in three-memberred rings | special |
| cv | sp2 C in four-memberred rings | special |
| cx | sp3 C in three-memberred rings | special |
| cy | sp3 C in four-memberred rings | special |
| n | aromatic nitrogen | special |
| nb | inner sp2 N in conjugated ring systems | special |
| nc(nd) | inner sp2 N in conjugated chain systems | special |
| sx | conjugated S, 3 substituted | special |
| sy | conjugated S, 4 substituted | special |
| pb | aromatic phosphorus | special |
| pc(pd) | inner sp2 P in conjugated ring systems | special |
| pe(pf) | inner sp2 P in conjugated chain systems | special |
| px | conjugated P, 3 substituted | special |
| py | conjugated P, 4 substituted | special |