diff CADDSuite-1.6/data/OpenBabel/gaff.prm @ 8:dbb480e39d95 draft

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author marcel
date Sat, 15 Dec 2012 13:15:46 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.6/data/OpenBabel/gaff.prm	Sat Dec 15 13:15:46 2012 -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](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    ""