RE: [AMBER] The PDB file was not recognized by Amber, what can i do?

From: Houyang Chen <houyangchen2008.hotmail.com>
Date: Wed, 29 Apr 2009 04:42:39 +0100

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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>
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Assistant professor
>
> NEW ADDRESS !!!
>
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> Laboratoire ITODYS
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> 75013 Paris FRANCE
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> 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 - 13:19:29 PDT
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