Hi Houyang,
PDB is an abbreviation for "protein data bank", therefore this file
format is employed for proteins and, more generally for
biomacromolecules. Apparently you want to study a carbon nanotube.
This compound is not directly parametrized on amber and this is why
you could not directly used your input file.
I already used amber molecular dynamics simulations for a molecule
with a C60 moiety. I made the parametrisation with gaussian
calculations and antechamber, and also other tricks to give the
correct atom types and parameters. You might find inspiration on the
tutorials.
Moreover, when I tried to open your pdb file on vmd it appears that
the z coordinates are badly placed (the molecule is on the same
plane). I think you will have to check if the coordinates are correct.
Regards,
Florent Barbault
On Wed, 29 Apr 2009 06:00:05 +0800
Houyang Chen <houyangchen2008.hotmail.com> wrote:
>
> Hi,everyone,
>
>
>
> I built a PDB file about carbon tube.
>
> However, it was not recognized by Amber, what can i do?
>
>
>
> Thanks
>
>
>
> Houyang
>
>
>
> =============================================
>
> REMARK PDB file
> REMARK Created:2009-4-28 17:58:25
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P1
> ATOM 1 C C A 1 3.887 0.000 0.000 1.00 0.00
> ATOM 2 C C A 1 3.697 1.201 2.115 1.00 0.00
> ATOM 3 C C A 1 3.887 0.000 1.410 1.00 0.00
> ATOM 4 C C A 1 3.697 1.201 3.525 1.00 0.00
> ATOM 5 C C A 1 3.887 0.000 4.230 1.00 0.00
> ATOM 6 C C A 1 3.697 1.201 6.345 1.00 0.00
> ATOM 7 C C A 1 3.887 0.000 5.640 1.00 0.00
> ATOM 8 C C A 1 3.697 1.201 7.755 1.00 0.00
> ATOM 9 C C A 1 3.887 0.000 8.460 1.00 0.00
> ATOM 10 C C A 1 3.697 1.201 10.575 1.00 0.00
> ATOM 11 C C A 1 3.887 0.000 9.870 1.00 0.00
> ATOM 12 C C A 1 3.697 1.201 11.985 1.00 0.00
> ATOM 13 C C A 1 3.887 0.000 12.690 1.00 0.00
> ATOM 14 C C A 1 3.697 1.201 14.805 1.00 0.00
> ATOM 15 C C A 1 3.887 0.000 14.100 1.00 0.00
> ATOM 16 C C A 1 3.697 1.201 16.215 1.00 0.00
> ATOM 17 C C A 1 3.887 0.000 16.920 1.00 0.00
> ATOM 18 C C A 1 3.697 1.201 19.035 1.00 0.00
> ATOM 19 C C A 1 3.887 0.000 18.330 1.00 0.00
> ATOM 20 C C A 1 3.697 1.201 20.445 1.00 0.00
> ATOM 21 C C A 1 3.887 0.000 21.150 1.00 0.00
> ATOM 22 C C A 1 3.697 1.201 23.265 1.00 0.00
> ATOM 23 C C A 1 3.887 0.000 22.560 1.00 0.00
> ATOM 24 C C A 1 3.697 1.201 24.675 1.00 0.00
> ATOM 25 C C A 1 3.145 2.285 0.000 1.00 0.00
> ATOM 26 C C A 1 2.285 3.145 2.115 1.00 0.00
> ATOM 27 C C A 1 3.145 2.285 1.410 1.00 0.00
> ATOM 28 C C A 1 2.285 3.145 3.525 1.00 0.00
> ATOM 29 C C A 1 3.145 2.285 4.230 1.00 0.00
> ATOM 30 C C A 1 2.285 3.145 6.345 1.00 0.00
> ATOM 31 C C A 1 3.145 2.285 5.640 1.00 0.00
> ATOM 32 C C A 1 2.285 3.145 7.755 1.00 0.00
> ATOM 33 C C A 1 3.145 2.285 8.460 1.00 0.00
> ATOM 34 C C A 1 2.285 3.145 10.575 1.00 0.00
> ATOM 35 C C A 1 3.145 2.285 9.870 1.00 0.00
> ATOM 36 C C A 1 2.285 3.145 11.985 1.00 0.00
> ATOM 37 C C A 1 3.145 2.285 12.690 1.00 0.00
> ATOM 38 C C A 1 2.285 3.145 14.805 1.00 0.00
> ATOM 39 C C A 1 3.145 2.285 14.100 1.00 0.00
> ATOM 40 C C A 1 2.285 3.145 16.215 1.00 0.00
> ATOM 41 C C A 1 3.145 2.285 16.920 1.00 0.00
> ATOM 42 C C A 1 2.285 3.145 19.035 1.00 0.00
> ATOM 43 C C A 1 3.145 2.285 18.330 1.00 0.00
> ATOM 44 C C A 1 2.285 3.145 20.445 1.00 0.00
> ATOM 45 C C A 1 3.145 2.285 21.150 1.00 0.00
> ATOM 46 C C A 1 2.285 3.145 23.265 1.00 0.00
> ATOM 47 C C A 1 3.145 2.285 22.560 1.00 0.00
> ATOM 48 C C A 1 2.285 3.145 24.675 1.00 0.00
> ATOM 49 C C A 1 1.201 3.697 0.000 1.00 0.00
> ATOM 50 C C A 1 0.000 3.887 2.115 1.00 0.00
> ATOM 51 C C A 1 1.201 3.697 1.410 1.00 0.00
> ATOM 52 C C A 1 0.000 3.887 3.525 1.00 0.00
> ATOM 53 C C A 1 1.201 3.697 4.230 1.00 0.00
> ATOM 54 C C A 1 0.000 3.887 6.345 1.00 0.00
> ATOM 55 C C A 1 1.201 3.697 5.640 1.00 0.00
> ATOM 56 C C A 1 0.000 3.887 7.755 1.00 0.00
> ATOM 57 C C A 1 1.201 3.697 8.460 1.00 0.00
> ATOM 58 C C A 1 0.000 3.887 10.575 1.00 0.00
> ATOM 59 C C A 1 1.201 3.697 9.870 1.00 0.00
> ATOM 60 C C A 1 0.000 3.887 11.985 1.00 0.00
> ATOM 61 C C A 1 1.201 3.697 12.690 1.00 0.00
> ATOM 62 C C A 1 0.000 3.887 14.805 1.00 0.00
> ATOM 63 C C A 1 1.201 3.697 14.100 1.00 0.00
> ATOM 64 C C A 1 0.000 3.887 16.215 1.00 0.00
> ATOM 65 C C A 1 1.201 3.697 16.920 1.00 0.00
> ATOM 66 C C A 1 0.000 3.887 19.035 1.00 0.00
> ATOM 67 C C A 1 1.201 3.697 18.330 1.00 0.00
> ATOM 68 C C A 1 0.000 3.887 20.445 1.00 0.00
> ATOM 69 C C A 1 1.201 3.697 21.150 1.00 0.00
> ATOM 70 C C A 1 0.000 3.887 23.265 1.00 0.00
> ATOM 71 C C A 1 1.201 3.697 22.560 1.00 0.00
> ATOM 72 C C A 1 0.000 3.887 24.675 1.00 0.00
> ATOM 73 C C A 1 -1.201 3.697 0.000 1.00 0.00
> ATOM 74 C C A 1 -2.285 3.145 2.115 1.00 0.00
> ATOM 75 C C A 1 -1.201 3.697 1.410 1.00 0.00
> ATOM 76 C C A 1 -2.285 3.145 3.525 1.00 0.00
> ATOM 77 C C A 1 -1.201 3.697 4.230 1.00 0.00
> ATOM 78 C C A 1 -2.285 3.145 6.345 1.00 0.00
> ATOM 79 C C A 1 -1.201 3.697 5.640 1.00 0.00
> ATOM 80 C C A 1 -2.285 3.145 7.755 1.00 0.00
> ATOM 81 C C A 1 -1.201 3.697 8.460 1.00 0.00
> ATOM 82 C C A 1 -2.285 3.145 10.575 1.00 0.00
> ATOM 83 C C A 1 -1.201 3.697 9.870 1.00 0.00
> ATOM 84 C C A 1 -2.285 3.145 11.985 1.00 0.00
> ATOM 85 C C A 1 -1.201 3.697 12.690 1.00 0.00
> ATOM 86 C C A 1 -2.285 3.145 14.805 1.00 0.00
> ATOM 87 C C A 1 -1.201 3.697 14.100 1.00 0.00
> ATOM 88 C C A 1 -2.285 3.145 16.215 1.00 0.00
> ATOM 89 C C A 1 -1.201 3.697 16.920 1.00 0.00
> ATOM 90 C C A 1 -2.285 3.145 19.035 1.00 0.00
> ATOM 91 C C A 1 -1.201 3.697 18.330 1.00 0.00
> ATOM 92 C C A 1 -2.285 3.145 20.445 1.00 0.00
> ATOM 93 C C A 1 -1.201 3.697 21.150 1.00 0.00
> ATOM 94 C C A 1 -2.285 3.145 23.265 1.00 0.00
> ATOM 95 C C A 1 -1.201 3.697 22.560 1.00 0.00
> ATOM 96 C C A 1 -2.285 3.145 24.675 1.00 0.00
> ATOM 97 C C A 1 -3.145 2.285 0.000 1.00 0.00
> ATOM 98 C C A 1 -3.697 1.201 2.115 1.00 0.00
> ATOM 99 C C A 1 -3.145 2.285 1.410 1.00 0.00
> ATOM 100 C C A 1 -3.697 1.201 3.525 1.00 0.00
> ATOM 101 C C A 1 -3.145 2.285 4.230 1.00 0.00
> ATOM 102 C C A 1 -3.697 1.201 6.345 1.00 0.00
> ATOM 103 C C A 1 -3.145 2.285 5.640 1.00 0.00
> ATOM 104 C C A 1 -3.697 1.201 7.755 1.00 0.00
> ATOM 105 C C A 1 -3.145 2.285 8.460 1.00 0.00
> ATOM 106 C C A 1 -3.697 1.201 10.575 1.00 0.00
> ATOM 107 C C A 1 -3.145 2.285 9.870 1.00 0.00
> ATOM 108 C C A 1 -3.697 1.201 11.985 1.00 0.00
> ATOM 109 C C A 1 -3.145 2.285 12.690 1.00 0.00
> ATOM 110 C C A 1 -3.697 1.201 14.805 1.00 0.00
> ATOM 111 C C A 1 -3.145 2.285 14.100 1.00 0.00
> ATOM 112 C C A 1 -3.697 1.201 16.215 1.00 0.00
> ATOM 113 C C A 1 -3.145 2.285 16.920 1.00 0.00
> ATOM 114 C C A 1 -3.697 1.201 19.035 1.00 0.00
> ATOM 115 C C A 1 -3.145 2.285 18.330 1.00 0.00
> ATOM 116 C C A 1 -3.697 1.201 20.445 1.00 0.00
> ATOM 117 C C A 1 -3.145 2.285 21.150 1.00 0.00
> ATOM 118 C C A 1 -3.697 1.201 23.265 1.00 0.00
> ATOM 119 C C A 1 -3.145 2.285 22.560 1.00 0.00
> ATOM 120 C C A 1 -3.697 1.201 24.675 1.00 0.00
> ATOM 121 C C A 1 -3.887 0.000 0.000 1.00 0.00
> ATOM 122 C C A 1 -3.697 -1.201 2.115 1.00 0.00
> ATOM 123 C C A 1 -3.887 0.000 1.410 1.00 0.00
> ATOM 124 C C A 1 -3.697 -1.201 3.525 1.00 0.00
> ATOM 125 C C A 1 -3.887 0.000 4.230 1.00 0.00
> ATOM 126 C C A 1 -3.697 -1.201 6.345 1.00 0.00
> ATOM 127 C C A 1 -3.887 0.000 5.640 1.00 0.00
> ATOM 128 C C A 1 -3.697 -1.201 7.755 1.00 0.00
> ATOM 129 C C A 1 -3.887 0.000 8.460 1.00 0.00
> ATOM 130 C C A 1 -3.697 -1.201 10.575 1.00 0.00
> ATOM 131 C C A 1 -3.887 0.000 9.870 1.00 0.00
> ATOM 132 C C A 1 -3.697 -1.201 11.985 1.00 0.00
> ATOM 133 C C A 1 -3.887 0.000 12.690 1.00 0.00
> ATOM 134 C C A 1 -3.697 -1.201 14.805 1.00 0.00
> ATOM 135 C C A 1 -3.887 0.000 14.100 1.00 0.00
> ATOM 136 C C A 1 -3.697 -1.201 16.215 1.00 0.00
> ATOM 137 C C A 1 -3.887 0.000 16.920 1.00 0.00
> ATOM 138 C C A 1 -3.697 -1.201 19.035 1.00 0.00
> ATOM 139 C C A 1 -3.887 0.000 18.330 1.00 0.00
> ATOM 140 C C A 1 -3.697 -1.201 20.445 1.00 0.00
> ATOM 141 C C A 1 -3.887 0.000 21.150 1.00 0.00
> ATOM 142 C C A 1 -3.697 -1.201 23.265 1.00 0.00
> ATOM 143 C C A 1 -3.887 0.000 22.560 1.00 0.00
> ATOM 144 C C A 1 -3.697 -1.201 24.675 1.00 0.00
> ATOM 145 C C A 1 -3.145 -2.285 0.000 1.00 0.00
> ATOM 146 C C A 1 -2.285 -3.145 2.115 1.00 0.00
> ATOM 147 C C A 1 -3.145 -2.285 1.410 1.00 0.00
> ATOM 148 C C A 1 -2.285 -3.145 3.525 1.00 0.00
> ATOM 149 C C A 1 -3.145 -2.285 4.230 1.00 0.00
> ATOM 150 C C A 1 -2.285 -3.145 6.345 1.00 0.00
> ATOM 151 C C A 1 -3.145 -2.285 5.640 1.00 0.00
> ATOM 152 C C A 1 -2.285 -3.145 7.755 1.00 0.00
> ATOM 153 C C A 1 -3.145 -2.285 8.460 1.00 0.00
> ATOM 154 C C A 1 -2.285 -3.145 10.575 1.00 0.00
> ATOM 155 C C A 1 -3.145 -2.285 9.870 1.00 0.00
> ATOM 156 C C A 1 -2.285 -3.145 11.985 1.00 0.00
> ATOM 157 C C A 1 -3.145 -2.285 12.690 1.00 0.00
> ATOM 158 C C A 1 -2.285 -3.145 14.805 1.00 0.00
> ATOM 159 C C A 1 -3.145 -2.285 14.100 1.00 0.00
> ATOM 160 C C A 1 -2.285 -3.145 16.215 1.00 0.00
> ATOM 161 C C A 1 -3.145 -2.285 16.920 1.00 0.00
> ATOM 162 C C A 1 -2.285 -3.145 19.035 1.00 0.00
> ATOM 163 C C A 1 -3.145 -2.285 18.330 1.00 0.00
> ATOM 164 C C A 1 -2.285 -3.145 20.445 1.00 0.00
> ATOM 165 C C A 1 -3.145 -2.285 21.150 1.00 0.00
> ATOM 166 C C A 1 -2.285 -3.145 23.265 1.00 0.00
> ATOM 167 C C A 1 -3.145 -2.285 22.560 1.00 0.00
> ATOM 168 C C A 1 -2.285 -3.145 24.675 1.00 0.00
> ATOM 169 C C A 1 -1.201 -3.697 0.000 1.00 0.00
> ATOM 170 C C A 1 0.000 -3.887 2.115 1.00 0.00
> ATOM 171 C C A 1 -1.201 -3.697 1.410 1.00 0.00
> ATOM 172 C C A 1 0.000 -3.887 3.525 1.00 0.00
> ATOM 173 C C A 1 -1.201 -3.697 4.230 1.00 0.00
> ATOM 174 C C A 1 0.000 -3.887 6.345 1.00 0.00
> ATOM 175 C C A 1 -1.201 -3.697 5.640 1.00 0.00
> ATOM 176 C C A 1 0.000 -3.887 7.755 1.00 0.00
> ATOM 177 C C A 1 -1.201 -3.697 8.460 1.00 0.00
> ATOM 178 C C A 1 0.000 -3.887 10.575 1.00 0.00
> ATOM 179 C C A 1 -1.201 -3.697 9.870 1.00 0.00
> ATOM 180 C C A 1 0.000 -3.887 11.985 1.00 0.00
> ATOM 181 C C A 1 -1.201 -3.697 12.690 1.00 0.00
> ATOM 182 C C A 1 0.000 -3.887 14.805 1.00 0.00
> ATOM 183 C C A 1 -1.201 -3.697 14.100 1.00 0.00
> ATOM 184 C C A 1 0.000 -3.887 16.215 1.00 0.00
> ATOM 185 C C A 1 -1.201 -3.697 16.920 1.00 0.00
> ATOM 186 C C A 1 0.000 -3.887 19.035 1.00 0.00
> ATOM 187 C C A 1 -1.201 -3.697 18.330 1.00 0.00
> ATOM 188 C C A 1 0.000 -3.887 20.445 1.00 0.00
> ATOM 189 C C A 1 -1.201 -3.697 21.150 1.00 0.00
> ATOM 190 C C A 1 0.000 -3.887 23.265 1.00 0.00
> ATOM 191 C C A 1 -1.201 -3.697 22.560 1.00 0.00
> ATOM 192 C C A 1 0.000 -3.887 24.675 1.00 0.00
> ATOM 193 C C A 1 1.201 -3.697 0.000 1.00 0.00
> ATOM 194 C C A 1 2.285 -3.145 2.115 1.00 0.00
> ATOM 195 C C A 1 1.201 -3.697 1.410 1.00 0.00
> ATOM 196 C C A 1 2.285 -3.145 3.525 1.00 0.00
> ATOM 197 C C A 1 1.201 -3.697 4.230 1.00 0.00
> ATOM 198 C C A 1 2.285 -3.145 6.345 1.00 0.00
> ATOM 199 C C A 1 1.201 -3.697 5.640 1.00 0.00
> ATOM 200 C C A 1 2.285 -3.145 7.755 1.00 0.00
> ATOM 201 C C A 1 1.201 -3.697 8.460 1.00 0.00
> ATOM 202 C C A 1 2.285 -3.145 10.575 1.00 0.00
> ATOM 203 C C A 1 1.201 -3.697 9.870 1.00 0.00
> ATOM 204 C C A 1 2.285 -3.145 11.985 1.00 0.00
> ATOM 205 C C A 1 1.201 -3.697 12.690 1.00 0.00
> ATOM 206 C C A 1 2.285 -3.145 14.805 1.00 0.00
> ATOM 207 C C A 1 1.201 -3.697 14.100 1.00 0.00
> ATOM 208 C C A 1 2.285 -3.145 16.215 1.00 0.00
> ATOM 209 C C A 1 1.201 -3.697 16.920 1.00 0.00
> ATOM 210 C C A 1 2.285 -3.145 19.035 1.00 0.00
> ATOM 211 C C A 1 1.201 -3.697 18.330 1.00 0.00
> ATOM 212 C C A 1 2.285 -3.145 20.445 1.00 0.00
> ATOM 213 C C A 1 1.201 -3.697 21.150 1.00 0.00
> ATOM 214 C C A 1 2.285 -3.145 23.265 1.00 0.00
> ATOM 215 C C A 1 1.201 -3.697 22.560 1.00 0.00
> ATOM 216 C C A 1 2.285 -3.145 24.675 1.00 0.00
> ATOM 217 C C A 1 3.145 -2.285 0.000 1.00 0.00
> ATOM 218 C C A 1 3.697 -1.201 2.115 1.00 0.00
> ATOM 219 C C A 1 3.145 -2.285 1.410 1.00 0.00
> ATOM 220 C C A 1 3.697 -1.201 3.525 1.00 0.00
> ATOM 221 C C A 1 3.145 -2.285 4.230 1.00 0.00
> ATOM 222 C C A 1 3.697 -1.201 6.345 1.00 0.00
> ATOM 223 C C A 1 3.145 -2.285 5.640 1.00 0.00
> ATOM 224 C C A 1 3.697 -1.201 7.755 1.00 0.00
> ATOM 225 C C A 1 3.145 -2.285 8.460 1.00 0.00
> ATOM 226 C C A 1 3.697 -1.201 10.575 1.00 0.00
> ATOM 227 C C A 1 3.145 -2.285 9.870 1.00 0.00
> ATOM 228 C C A 1 3.697 -1.201 11.985 1.00 0.00
> ATOM 229 C C A 1 3.145 -2.285 12.690 1.00 0.00
> ATOM 230 C C A 1 3.697 -1.201 14.805 1.00 0.00
> ATOM 231 C C A 1 3.145 -2.285 14.100 1.00 0.00
> ATOM 232 C C A 1 3.697 -1.201 16.215 1.00 0.00
> ATOM 233 C C A 1 3.145 -2.285 16.920 1.00 0.00
> ATOM 234 C C A 1 3.697 -1.201 19.035 1.00 0.00
> ATOM 235 C C A 1 3.145 -2.285 18.330 1.00 0.00
> ATOM 236 C C A 1 3.697 -1.201 20.445 1.00 0.00
> ATOM 237 C C A 1 3.145 -2.285 21.150 1.00 0.00
> ATOM 238 C C A 1 3.697 -1.201 23.265 1.00 0.00
> ATOM 239 C C A 1 3.145 -2.285 22.560 1.00 0.00
> ATOM 240 C C A 1 3.697 -1.201 24.675 1.00 0.00
> TER
>
>
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-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
NEW ADDRESS !!!
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baf, btiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
-------------------------------------------------
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Received on Wed May 20 2009 - 13:17:47 PDT
