1; 2; File 'topol.top' was generated 3; By user: onbekend (0) 4; On host: onbekend 5; At date: Tue Aug 10 18:52:18 2010 6; 7; This is your topology file 8; it was generated using program: 9; pdb2gmx - version 4.5-beta2 10; with command line: 11; pdb2gmx -f charmm.pdb -inter 12; 13 14; Include forcefield parameters 15#include "charmm27.ff/forcefield.itp" 16 17[ moleculetype ] 18; Name nrexcl 19Other 3 20 21[ atoms ] 22; nr type resnr residue atom cgnr charge mass typeB chargeB massB 23; residue 1 ALAD rtp ALAD q 0.0 24 1 CT3 1 ALAD CL 1 -0.27 12.011 ; qtot -0.27 25 2 HA 1 ALAD HL1 1 0.09 1.008 ; qtot -0.18 26 3 HA 1 ALAD HL2 1 0.09 1.008 ; qtot -0.09 27 4 HA 1 ALAD HL3 1 0.09 1.008 ; qtot 0 28 5 C 1 ALAD CLP 2 0.51 12.011 ; qtot 0.51 29 6 O 1 ALAD OL 2 -0.51 15.999 ; qtot 0 30 7 NH1 1 ALAD NL 3 -0.47 14.007 ; qtot -0.47 31 8 H 1 ALAD HL 3 0.31 1.008 ; qtot -0.16 32 9 CT1 1 ALAD CA 3 0.07 12.011 ; qtot -0.09 33 10 HB 1 ALAD HA 3 0.09 1.008 ; qtot 0 34 11 CT3 1 ALAD CB 4 -0.27 12.011 ; qtot -0.27 35 12 HA 1 ALAD HB1 4 0.09 1.008 ; qtot -0.18 36 13 HA 1 ALAD HB2 4 0.09 1.008 ; qtot -0.09 37 14 HA 1 ALAD HB3 4 0.09 1.008 ; qtot 0 38 15 C 1 ALAD CRP 5 0.51 12.011 ; qtot 0.51 39 16 O 1 ALAD OR 5 -0.51 15.999 ; qtot 0 40 17 NH1 1 ALAD NR 6 -0.47 14.007 ; qtot -0.47 41 18 H 1 ALAD HR 6 0.31 1.008 ; qtot -0.16 42 19 CT3 1 ALAD CR 6 -0.11 12.011 ; qtot -0.27 43 20 HA 1 ALAD HR1 6 0.09 1.008 ; qtot -0.18 44 21 HA 1 ALAD HR2 6 0.09 1.008 ; qtot -0.09 45 22 HA 1 ALAD HR3 6 0.09 1.008 ; qtot 0 46 47[ bonds ] 48; ai aj funct c0 c1 c2 c3 49 1 2 1 50 1 3 1 51 1 4 1 52 1 5 1 53 5 6 1 54 5 7 1 55 7 8 1 56 7 9 1 57 9 10 1 58 9 11 1 59 9 15 1 60 11 12 1 61 11 13 1 62 11 14 1 63 15 16 1 64 15 17 1 65 17 18 1 66 17 19 1 67 19 20 1 68 19 21 1 69 19 22 1 70 71[ pairs ] 72; ai aj funct c0 c1 c2 c3 73 1 8 1 74 1 9 1 75 2 6 1 76 2 7 1 77 3 6 1 78 3 7 1 79 4 6 1 80 4 7 1 81 5 10 1 82 5 11 1 83 5 15 1 84 6 8 1 85 6 9 1 86 7 12 1 87 7 13 1 88 7 14 1 89 7 16 1 90 7 17 1 91 8 10 1 92 8 11 1 93 8 15 1 94 9 18 1 95 9 19 1 96 10 12 1 97 10 13 1 98 10 14 1 99 10 16 1 100 10 17 1 101 11 16 1 102 11 17 1 103 12 15 1 104 13 15 1 105 14 15 1 106 15 20 1 107 15 21 1 108 15 22 1 109 16 18 1 110 16 19 1 111 18 20 1 112 18 21 1 113 18 22 1 114 115[ angles ] 116; ai aj ak funct c0 c1 c2 c3 117 2 1 3 5 118 2 1 4 5 119 2 1 5 5 120 3 1 4 5 121 3 1 5 5 122 4 1 5 5 123 1 5 6 5 124 1 5 7 5 125 6 5 7 5 126 5 7 8 5 127 5 7 9 5 128 8 7 9 5 129 7 9 10 5 130 7 9 11 5 131 7 9 15 5 132 10 9 11 5 133 10 9 15 5 134 11 9 15 5 135 9 11 12 5 136 9 11 13 5 137 9 11 14 5 138 12 11 13 5 139 12 11 14 5 140 13 11 14 5 141 9 15 16 5 142 9 15 17 5 143 16 15 17 5 144 15 17 18 5 145 15 17 19 5 146 18 17 19 5 147 17 19 20 5 148 17 19 21 5 149 17 19 22 5 150 20 19 21 5 151 20 19 22 5 152 21 19 22 5 153 154[ dihedrals ] 155; ai aj ak al funct c0 c1 c2 c3 c4 c5 156 2 1 5 6 9 157 2 1 5 7 9 158 3 1 5 6 9 159 3 1 5 7 9 160 4 1 5 6 9 161 4 1 5 7 9 162 1 5 7 8 9 163 1 5 7 9 9 164 6 5 7 8 9 165 6 5 7 9 9 166 5 7 9 10 9 167 5 7 9 11 9 168 5 7 9 15 9 169 8 7 9 10 9 170 8 7 9 11 9 171 8 7 9 15 9 172 7 9 11 12 9 173 7 9 11 13 9 174 7 9 11 14 9 175 10 9 11 12 9 176 10 9 11 13 9 177 10 9 11 14 9 178 15 9 11 12 9 179 15 9 11 13 9 180 15 9 11 14 9 181 7 9 15 16 9 182 7 9 15 17 9 183 10 9 15 16 9 184 10 9 15 17 9 185 11 9 15 16 9 186 11 9 15 17 9 187 9 15 17 18 9 188 9 15 17 19 9 189 16 15 17 18 9 190 16 15 17 19 9 191 15 17 19 20 9 192 15 17 19 21 9 193 15 17 19 22 9 194 18 17 19 20 9 195 18 17 19 21 9 196 18 17 19 22 9 197 198[ dihedrals ] 199; ai aj ak al funct c0 c1 c2 c3 200 5 1 7 6 2 201 7 5 9 8 2 202 15 9 17 16 2 203 17 15 19 18 2 204 205; Include Position restraint file 206#ifdef POSRES 207#include "posre.itp" 208#endif 209 210[ system ] 211; Name 212ALANINE DIPEPTIDE 213 214[ molecules ] 215; Compound #mols 216Other 1 217