Mercurial > repos > marcel > caddsuite_linux_x86_64
view CADDSuite-1.0.1/data/OpenBabel/gaff.prm @ 9:2cff9609f2c7
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:40:26 -0500 |
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// // 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]=[O,S] c "C=O or C=S" atom [#6X3](N)(N)N cz "" 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 ring systems" atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated ring systems" atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated ring 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 [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 ""