Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite/data/OpenBabel/gaff.prm @ 0:bac3c274238f
Migrated tool version 0.93 from old tool shed archive to new tool shed repository
| author | marcel |
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| date | Tue, 07 Jun 2011 16:43:30 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/gaff.prm Tue Jun 07 16:43:30 2011 -0400 @@ -0,0 +1,222 @@ +// +// 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]=[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 ""