Thanks.
Hi, Florent Barbault,
Can you tell me more detail about "made the parametrisation with gaussian
calculations and antechamber"?
Besides, which tutorials can show me more details?
By the way, i attached pdb file which i am able to load it in VMD.
Thanks.
Houyang
> From: florent.barbault.univ-paris-diderot.fr
> Subject: Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
> To: amber.ambermd.org
> Date: Wed, 29 Apr 2009 01:00:55 +0200
>
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> -------------------------------------------------
> 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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_________________________________________________________________
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Received on Wed May 20 2009 - 13:19:29 PDT
