MacroModel Atom Types

The following table lists the atom types that are used in MacroModel and their equivalencies to atom types for other force fields. These atom types are defined in the atom.typ file. See The atom.typ File for a description of the atom.typ file and how to add atom types.

Note that in MacroModel, 00 atoms are stored as type 0 in the atom connection table, and that all current force fields require explicit hydrogens on heteroatoms.

Table 1. Atom types and equivalents
No.	Symbol	Description	Equivalencies
No.	Symbol	Description	MM2/ MM3	Charmm	Amber
1	C1	Carbon - sp
2	C2	Carbon - sp²	2,3	CT,C	C, C*, CA, CB, CC, CM, CF, CG, CN
3	C3	Carbon - sp³	1	CT	CT
4	CA	United atom CH - sp³		CH1E	CH
5	CB	United atom CH₂ - sp³		CH2E	C2
6	CC	United atom CH₃ - sp³		CH3E	C3
7	CD	United atom CH - sp²		CR1E	CD, CE, CJ, CP
8	CE	United atom CH₂ - sp²
9	CF	United atom CH - sp
10	CM	Carbanion (C⁻)
11	CP	Carbocation (C⁺)	30
12	CR	Carbon free radical	29
...
14	C0	Any carbon
15	O2	Oxygen - double bond	7	O	O, O2
16	O3	Oxygen - single bond	6	OH1, OH2	OS, OH
17	OA	United atom OH		OH1E
18	OM	O^- (alkoxide, carboxylate)	47		OC
19	OW	United atom H₂O		OH2E
20	OP	Oxonium (sp²) =[O⁺]–
21	OQ	Oxonium (sp³) R₃O⁺
...
23	O0	Any oxygen
24	N1	Nitrogen - sp	10
25	N2	Nitrogen - sp²	9	N, NR, NP, NH1, NH2	N, NB, NC, N*, N2
26	N3	Nitrogen - sp³	8	NH3	NT
27	NA	United atom NH - sp³
28	NB	United atom NH₂ - sp³		NH1E
29	NC	United atom NH - sp²
30	ND	United atom NH₂ - sp²		NH2E
31	N4	N⁺ - sp²		NC2	NA
32	N5	N⁺ - sp³	39		N3
33	NE	United atom NH⁺ - sp³
34	NF	United atom NH₂⁺ - sp³
35	NG	United atom NH₃⁺ - sp³		NH3E
36	NH	United atom NH⁺ - sp²
37	NI	United atom NH₂⁺ - sp²		NC2E
38	NM	N⁻ - sp³
39	NP	N⁻ - sp²
40	N0	Any nitrogen
41	H1	H-Electroneut(e.g., C,S)	5, 44	HA	HC, HS
42	H2	H-O (Neutral)	21, 24	H,HC	HO
43	H3	H-N (Neutral)	23, 28	H,HC	H, H2
44	H4	H⁺ (Cation)	48 MM3 (none in MM2)		H3
45	H5	H⁻ (Anion)
...
48	H0	Any hydrogen
49	S1	Sulfur	15,17,18	S	S, SH
50	SA	United atom SH		SH1E
51	SM	S⁻ (thiolate anion)
52	S0	Any Sulfur		S
53	P3	Phosphorus, trivalent	25		P
54	B2	Boron - sp²	26
55	B3	Boron - sp³	27
56	F0	Fluorine	11
57	Cl	Chlorine	12
58	Br	Bromine	13
59	I0	Iodine	14
60	Si	Silicon	19
61	Du	Dummy atom for FEP
62	Z0	Special atom to be defined
63	Lp	Lone electron pair			LP
64	00	Any atom	0	*
65	Li	Li⁺			Li
66	Na	Na⁺		SOD	Na
67	K0	K⁺		POT	K0
68	Rb	Rb⁺			Rb
69	Cs	Cs⁺		CES
70	Ca	Ca⁺²		CAL
71	Ba	Ba⁺²
72	Mg	Mg⁺²		MG
73	M2	Mn⁺²
74	M3	Mn⁺³
75	M4	Mn⁺⁴
76	M5	Mn⁺⁵
77	M6	Mn⁺⁶
78	M7	Mn⁺⁷
79	f2	Fe⁺²
80	f3	Fe⁺³
81	o2	Co⁺²
82	o3	Co⁺³
83	n2	Ni⁺²
84	n3	Ni⁺³
85	c1	Cu⁺
86	c2	Cu⁺²
87	Zn	Zn⁺²
88	m3	Mo⁺³
89	m4	Mo⁺⁴
90	m5	Mo⁺⁵
91	m6	Mo⁺⁶
92	Sr	Sr⁺²
93	L0	Lithium neutral
94	M0	Magnesium neutral
95	As	Arsenic, pentavalent tetrahedral (e.g. AsO₄³⁻)
96	A3	Arsenic, trivalent
...
100	SP	S⁺
101	S2	Sulfur - sp²
102	Cm	Cl⁻		CLA
103	B0	Any boron
104	Fm	F⁻
105	Bm	Br⁻
106	Im	I⁻
107	P5	Phosphorus, pentavalent tetrahedral (e.g. PO₄³⁻)
108	P0	Any phosphorus
109	S4	Sulfur, tetravalent
110	S6	Sulfur, hexavalent octahedral (e.g. SF₆)
111	P4	P⁺, tetravalent
112	Se	Selenium
113	ST	Sulfur, hexavalent tetrahedral (e.g. SO₄²⁻)
114	Sm	Sulfide anion, S²⁻
115	Om	Oxide anion, O²⁻
...
150	PI	Ligand dummy atom

Table 2. Generalized atom types
No.	Symbol	Description
No.	Symbol	Description
151	GA	Isolated atom
152	GB	Linear-single coordinate
153	GC	Linear-two coordinate
154	GD	Trigonal-two coordinate
155	GE	Trigonal-three coordinate
156	GF	Tetrahedral-three coordinate
157	GG	Tetrahedral-four coordinate
158	GH	Trigonal bipyramid-three coordinate
159	GI	Trigonal bipyramid-four coordinate
160	GJ	Trigonal bipyramid-five coordinate
161	GK	Octahedral-four coordinate
162	GL	Octahedral-five coordinate
163	GM	Octahedral-six coordinate
164	GN	Pentagonal bipyramid-seven coordinate
165	GO	Twisted cube-eight coordinate
166	GP	Nine coordinate
167	GQ	Ten coordinate
168	GR	Eleven coordinate
169	GS	Icosahedron-twelve coordinate
170	GT	Thirteen coordinate
171	GU	Fourteen coordinate
172	GV	Fifteen coordinate
173	GW	Sixteen coordinate