Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite-1.6/data/OpenBabel/gaff.prm @ 10:eda78e0f5df6 draft default tip
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| author | marcel |
|---|---|
| date | Sun, 30 Nov 2014 03:46:08 -0500 |
| parents | 488032d372e1 |
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--- a/CADDSuite-1.6/data/OpenBabel/gaff.prm Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,222 +0,0 @@ -// -// 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 ""