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author marcel
date Sun, 30 Nov 2014 03:46:08 -0500
parents 488032d372e1
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9:488032d372e1 10:eda78e0f5df6
1 //
2 // Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
3 //
4 // This is a SMARTS template-file for GAFF-atom types
5 //
6 // It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"
7 // file included with the antechamber package of amber10.
8 // There is no 1-to-1 correspondence between the ATD format and SMARTS.
9 // Therefore the current definitions need to be tested and possibly changed
10 //
11 //
12 //
13 // GAFF atomtypes defined using SMARTS
14 // [SMARTS] [atomtype id number] [description]
15 // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
16 //
17 // Be careful lines do not exceed the maximum length of 80!
18
19 atom [*] X
20 atom [#1X1] ha "other hydrogen e.g. on aromatic C"
21 atom [#1X1][CX4] hc "hydrogen on aliphatic C"
22 // "hydrogen on aliphatic C with 1 ewd"
23 atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1
24 // "hydrogen on aliphatic C with 2 ewd"
25 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2
26 // "hydrogen on aliphatic C with 3 ewd"
27 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3
28 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3
29 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3
30 // "hydrogen on sp2 C with 1 ewd"
31 atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4
32 // "hydrogen on sp2 C with 2 ewd"
33 atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5
34 atom [#1X1][#6](N)(N)(N)N hx ""
35 atom [#1X1]O ho "hydrogen on oxygen"
36 atom [#1X1][Oh1] hw "hydrogen on water"
37 atom [#1X1]N hn "nitrogen"
38 atom [#1X1]S hs "sulphur"
39 atom [#1X1]P hp "phosphor"
40 atom [#6X4] c3 "other sp3 C"
41 atom [#6X4r3] cx "3-membered ring atom"
42 atom [#6X4r4] cy "4-membered ring atom"
43 atom [#6X3] c2 "other sp2 C"
44 atom [#6X3](N)(N)N cz "guanidine carbon"
45 atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems"
46 atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems"
47 atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems"
48 atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated chain systems"
49 atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated chain systems"
50 atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated chain systems"
51 atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system"
52 atom [#6X3r3] cu "sp2 carbon in a 3-membered ring"
53 atom [#6X3r4] cv "sp2 carbon in a 4-membered ring"
54 atom [#6X3]=[O,S] c "C=O or C=S"
55 atom [c] ca "pure aromatic atom"
56 atom [#6X2] c1 "other sp C"
57 atom [#6X2](=*)-*=* cg "sp C of conjugated system"
58 atom [#6X2](#*)-*=* cg "sp C of conjugated system"
59 atom [#6X2](#*)-*#* cg "sp C of conjugated system"
60 atom [#6X1] c1 "other sp C"
61
62 atom [F]* f (-*) "general fluorine"
63 atom [Cl]* cl (-*) "general chlorine"
64 atom [Br]* br (-*) "general bromine"
65 atom [I]* i (-*) "general iodine"
66
67 atom [#15X1] p2 "other sp2 P"
68 atom [#15X2] p2 "other sp2 P"
69 atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems"
70 atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems"
71 atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems"
72 atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system"
73 atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system"
74 atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system"
75 atom [#15;a] pb "aromatic P"
76 atom [#15X3] p3 "other sp3 P"
77 atom [#15X3](=*)-*=* px "sp2 P of conjugated system"
78 atom [#15X3](=*)-*#* px "sp2 P of conjugated system"
79 atom [#15X3]=[O,S] p4 "hypervalent P"
80 atom [#15X4] p5 "hypervalent P"
81 atom [#15X4](=*)-*=* py "P of conjugated system"
82 atom [#15X4](=*)-*#* py "P of conjugated system"
83 atom [#15X5] p5 "hypervalent P"
84 atom [#15X6] p5 "hypervalent P"
85
86 atom [#7X1] n1 "sp1 N"
87
88 atom [#7X2] n2 "sp2 N"
89 atom [#7X2](=*)=* n1 "sp1 N"
90 atom [#7X2](-*)#* n1 "sp1 N"
91 atom [#7X2;R](=*)-*=* nc "inner sp2 N of conjugated ring systems"
92 atom [#7X2;R](=*)-*#* nc "inner sp2 N of conjugated ring systems"
93 atom [#7X2;R](#*)-*#* nc "inner sp2 N of conjugated ring systems"
94 atom [#7X2;!R](=*)-*=* ne "inner sp2 N of conjugated chain system"
95 atom [#7X2;!R](=*)-*#* ne "inner sp2 N of conjugated chain system"
96 atom [#7X2;!R](#*)-*#* ne "inner sp2 N of conjugated chain system"
97 atom [nX2] nb "aromatic N"
98
99 atom [#7X3] n3 "sp3 N"
100 atom [#7X3]a nh "amine N connected to aromatic ring"
101 atom [#7X3]=[CX3] nh ""
102 atom [#7X3]=[N2] nh ""
103 atom [#7X3]=[P2] nh ""
104 atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides"
105 atom [#7X3](O)O no "N in nitro group"
106 atom [nX3] na "aromatic N"
107
108 atom [#7X4] n4 "sp3 N"
109
110 atom [OX1] o "sp2 O"
111 atom [OX2] os "sp3 O in esters and ethers"
112 atom [OX3] os "sp3 O in esters and ethers"
113 atom [OX2H] oh "sp3 O in hydroxyl group"
114 atom [OX3H] oh "sp3 O in hydroxyl group"
115
116 atom [SX1] s ""
117 atom [SX2] ss "sp3 sulphur"
118 atom [SX2]=* s2 "sp2 sulphur"
119 atom [SX2]#* s2 "sp2 sulphur"
120 atom [SX2H] sh "sp3 S in thiol"
121 atom [SX3] s4 "hypervalent S"
122 atom [SX3](=*)-*=* sx "conjugated S"
123 atom [SX3](=*)-*#* sx "conjugated S"
124 atom [SX4] s6 "hypervalent S"
125 atom [SX4](=*)-*=* sy "conjugated S"
126 atom [SX4](=*)-*#* sy "conjugated S"
127 atom [SX5] s6 "hypervalent S"
128 atom [SX6] s6 "hypervalent S"
129
130 atom [He] He ""
131 atom [Li] Li ""
132 atom [Be] Be ""
133 atom [B] B ""
134 atom [Ne] Ne ""
135 atom [Na] Na ""
136 atom [Mg] Mg ""
137 atom [Al] Al ""
138 atom [Si] Si ""
139 atom [Ar] Ar ""
140 atom [K] K ""
141 atom [Ca] Ca ""
142 atom [Sc] Sc ""
143 atom [Ti] Ti ""
144 atom [V] V ""
145 atom [Cr] Cr ""
146 atom [Mn] Mn ""
147 atom [Fe] Fe ""
148 atom [Co] Co ""
149 atom [Ni] Ni ""
150 atom [Cu] Cu ""
151 atom [Zn] Zn ""
152 atom [Ga] Ga ""
153 atom [Ge] Ge ""
154 atom [As] As ""
155 atom [Se] Se ""
156 atom [Kr] Kr ""
157 atom [Rb] Rb ""
158 atom [Sr] Sr ""
159 atom [Y] Y ""
160 atom [Zr] Zr ""
161 atom [Nb] Nb ""
162 atom [Mo] Mo ""
163 atom [Tc] Tc ""
164 atom [Ru] Ru ""
165 atom [Rh] Rh ""
166 atom [Pd] Pd ""
167 atom [Ag] Ag ""
168 atom [Cd] Cd ""
169 atom [In] In ""
170 atom [Sn] Sn ""
171 atom [Sb] Sb ""
172 atom [Te] Te ""
173 atom [Xe] Xe ""
174 atom [Cs] Cs ""
175 atom [Ba] Ba ""
176 atom [La] La ""
177 atom [Ce] Ce ""
178 atom [Pr] Pr ""
179 atom [Nd] Nd ""
180 atom [Pm] Pm ""
181 atom [Sm] Sm ""
182 atom [Eu] Eu ""
183 atom [Gd] Gd ""
184 atom [Tb] Tb ""
185 atom [Dy] Dy ""
186 atom [Ho] Ho ""
187 atom [Er] Er ""
188 atom [Tm] Tm ""
189 atom [Yb] Yb ""
190 atom [Lu] Lu ""
191 atom [Hf] Hf ""
192 atom [Ta] Ta ""
193 atom [W] W ""
194 atom [Re] Re ""
195 atom [Os] Os ""
196 atom [Ir] Ir ""
197 atom [Pt] Pt ""
198 atom [Au] Au ""
199 atom [Hg] Hg ""
200 atom [Tl] Tl ""
201 atom [Pb] Pb ""
202 atom [Bi] Bi ""
203 atom [Po] Po ""
204 atom [At] At ""
205 atom [Rn] Rn ""
206 atom [Fr] Fr ""
207 atom [Ra] Ra ""
208 atom [Ac] Ac ""
209 atom [Th] Th ""
210 atom [Pa] Pa ""
211 atom [U] U ""
212 atom [Np] Np ""
213 atom [Pu] Pu ""
214 atom [Am] Am ""
215 atom [Cm] Cm ""
216 atom [Bk] Bk ""
217 atom [Cf] Cf ""
218 atom [Es] Es ""
219 atom [Fm] Fm ""
220 atom [Md] Md ""
221 atom [No] No ""
222 atom [Lr] Lr ""