/usr/share/openbabel/2.3.2/gaff.prm is in libopenbabel4 2.3.2+dfsg-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 | //
// Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
//
// This is a SMARTS template-file for GAFF-atom types
//
// It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"
// file included with the antechamber package of amber10.
// There is no 1-to-1 correspondence between the ATD format and SMARTS.
// Therefore the current definitions need to be tested and possibly changed
//
//
//
// GAFF atomtypes defined using SMARTS
// [SMARTS] [atomtype id number] [description]
// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
//
// Be careful lines do not exceed the maximum length of 80!
atom [*] X
atom [#1X1] ha "other hydrogen e.g. on aromatic C"
atom [#1X1][CX4] hc "hydrogen on aliphatic C"
// "hydrogen on aliphatic C with 1 ewd"
atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1
// "hydrogen on aliphatic C with 2 ewd"
atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2
// "hydrogen on aliphatic C with 3 ewd"
atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3
atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3
atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3
// "hydrogen on sp2 C with 1 ewd"
atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4
// "hydrogen on sp2 C with 2 ewd"
atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5
atom [#1X1][#6](N)(N)(N)N hx ""
atom [#1X1]O ho "hydrogen on oxygen"
atom [#1X1][Oh1] hw "hydrogen on water"
atom [#1X1]N hn "nitrogen"
atom [#1X1]S hs "sulphur"
atom [#1X1]P hp "phosphor"
atom [#6X4] c3 "other sp3 C"
atom [#6X4r3] cx "3-membered ring atom"
atom [#6X4r4] cy "4-membered ring atom"
atom [#6X3] c2 "other sp2 C"
atom [#6X3](N)(N)N cz "guanidine carbon"
atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems"
atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems"
atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems"
atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated chain systems"
atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated chain systems"
atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated chain systems"
atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system"
atom [#6X3r3] cu "sp2 carbon in a 3-membered ring"
atom [#6X3r4] cv "sp2 carbon in a 4-membered ring"
atom [#6X3]=[O,S] c "C=O or C=S"
atom [c] ca "pure aromatic atom"
atom [#6X2] c1 "other sp C"
atom [#6X2](=*)-*=* cg "sp C of conjugated system"
atom [#6X2](#*)-*=* cg "sp C of conjugated system"
atom [#6X2](#*)-*#* cg "sp C of conjugated system"
atom [#6X1] c1 "other sp C"
atom [F]* f (-*) "general fluorine"
atom [Cl]* cl (-*) "general chlorine"
atom [Br]* br (-*) "general bromine"
atom [I]* i (-*) "general iodine"
atom [#15X1] p2 "other sp2 P"
atom [#15X2] p2 "other sp2 P"
atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems"
atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems"
atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems"
atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system"
atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system"
atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system"
atom [#15;a] pb "aromatic P"
atom [#15X3] p3 "other sp3 P"
atom [#15X3](=*)-*=* px "sp2 P of conjugated system"
atom [#15X3](=*)-*#* px "sp2 P of conjugated system"
atom [#15X3]=[O,S] p4 "hypervalent P"
atom [#15X4] p5 "hypervalent P"
atom [#15X4](=*)-*=* py "P of conjugated system"
atom [#15X4](=*)-*#* py "P of conjugated system"
atom [#15X5] p5 "hypervalent P"
atom [#15X6] p5 "hypervalent P"
atom [#7X1] n1 "sp1 N"
atom [#7X2] n2 "sp2 N"
atom [#7X2](=*)=* n1 "sp1 N"
atom [#7X2](-*)#* n1 "sp1 N"
atom [#7X2;R](=*)-*=* nc "inner sp2 N of conjugated ring systems"
atom [#7X2;R](=*)-*#* nc "inner sp2 N of conjugated ring systems"
atom [#7X2;R](#*)-*#* nc "inner sp2 N of conjugated ring systems"
atom [#7X2;!R](=*)-*=* ne "inner sp2 N of conjugated chain system"
atom [#7X2;!R](=*)-*#* ne "inner sp2 N of conjugated chain system"
atom [#7X2;!R](#*)-*#* ne "inner sp2 N of conjugated chain system"
atom [nX2] nb "aromatic N"
atom [#7X3] n3 "sp3 N"
atom [#7X3]a nh "amine N connected to aromatic ring"
atom [#7X3]=[CX3] nh ""
atom [#7X3]=[N2] nh ""
atom [#7X3]=[P2] nh ""
atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides"
atom [#7X3](O)O no "N in nitro group"
atom [nX3] na "aromatic N"
atom [#7X4] n4 "sp3 N"
atom [OX1] o "sp2 O"
atom [OX2] os "sp3 O in esters and ethers"
atom [OX3] os "sp3 O in esters and ethers"
atom [OX2H] oh "sp3 O in hydroxyl group"
atom [OX3H] oh "sp3 O in hydroxyl group"
atom [SX1] s ""
atom [SX2] ss "sp3 sulphur"
atom [SX2]=* s2 "sp2 sulphur"
atom [SX2]#* s2 "sp2 sulphur"
atom [SX2H] sh "sp3 S in thiol"
atom [SX3] s4 "hypervalent S"
atom [SX3](=*)-*=* sx "conjugated S"
atom [SX3](=*)-*#* sx "conjugated S"
atom [SX4] s6 "hypervalent S"
atom [SX4](=*)-*=* sy "conjugated S"
atom [SX4](=*)-*#* sy "conjugated S"
atom [SX5] s6 "hypervalent S"
atom [SX6] s6 "hypervalent S"
atom [He] He ""
atom [Li] Li ""
atom [Be] Be ""
atom [B] B ""
atom [Ne] Ne ""
atom [Na] Na ""
atom [Mg] Mg ""
atom [Al] Al ""
atom [Si] Si ""
atom [Ar] Ar ""
atom [K] K ""
atom [Ca] Ca ""
atom [Sc] Sc ""
atom [Ti] Ti ""
atom [V] V ""
atom [Cr] Cr ""
atom [Mn] Mn ""
atom [Fe] Fe ""
atom [Co] Co ""
atom [Ni] Ni ""
atom [Cu] Cu ""
atom [Zn] Zn ""
atom [Ga] Ga ""
atom [Ge] Ge ""
atom [As] As ""
atom [Se] Se ""
atom [Kr] Kr ""
atom [Rb] Rb ""
atom [Sr] Sr ""
atom [Y] Y ""
atom [Zr] Zr ""
atom [Nb] Nb ""
atom [Mo] Mo ""
atom [Tc] Tc ""
atom [Ru] Ru ""
atom [Rh] Rh ""
atom [Pd] Pd ""
atom [Ag] Ag ""
atom [Cd] Cd ""
atom [In] In ""
atom [Sn] Sn ""
atom [Sb] Sb ""
atom [Te] Te ""
atom [Xe] Xe ""
atom [Cs] Cs ""
atom [Ba] Ba ""
atom [La] La ""
atom [Ce] Ce ""
atom [Pr] Pr ""
atom [Nd] Nd ""
atom [Pm] Pm ""
atom [Sm] Sm ""
atom [Eu] Eu ""
atom [Gd] Gd ""
atom [Tb] Tb ""
atom [Dy] Dy ""
atom [Ho] Ho ""
atom [Er] Er ""
atom [Tm] Tm ""
atom [Yb] Yb ""
atom [Lu] Lu ""
atom [Hf] Hf ""
atom [Ta] Ta ""
atom [W] W ""
atom [Re] Re ""
atom [Os] Os ""
atom [Ir] Ir ""
atom [Pt] Pt ""
atom [Au] Au ""
atom [Hg] Hg ""
atom [Tl] Tl ""
atom [Pb] Pb ""
atom [Bi] Bi ""
atom [Po] Po ""
atom [At] At ""
atom [Rn] Rn ""
atom [Fr] Fr ""
atom [Ra] Ra ""
atom [Ac] Ac ""
atom [Th] Th ""
atom [Pa] Pa ""
atom [U] U ""
atom [Np] Np ""
atom [Pu] Pu ""
atom [Am] Am ""
atom [Cm] Cm ""
atom [Bk] Bk ""
atom [Cf] Cf ""
atom [Es] Es ""
atom [Fm] Fm ""
atom [Md] Md ""
atom [No] No ""
atom [Lr] Lr ""
|