[gmx-users] regarding x2top error
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 19 07:33:23 CET 2011
On 2011-12-19 07:15, priya thiyagarajan wrote:
> hello sir,
> i tried to produce rtp file using x2top command for my file
> HETATM 123 C BFC A 1 0.446 -0.085 2.419 1.00
> 0.00 C
> HETATM 124 O BFC A 1 0.234 -0.665 3.482 1.00
> 0.00 O
> HETATM 125 CA BFC A 1 1.485 -0.637 1.467 1.00
> 0.00 C
> HETATM 126 CB BFC A 1 1.895 0.310 0.300 1.00
> 0.00 C
> HETATM 127 OB BFC A 1 0.871 0.428 -0.648 1.00
> 0.00 O
> HETATM 128 CC BFC A 1 3.158 -0.281 -0.373 1.00
> 0.00 C
> HETATM 129 CD BFC A 1 3.913 0.725 -1.260 1.00
> 0.00 C
> HETATM 130 CE BFC A 1 4.740 1.741 -0.452 1.00
> 0.00 C
> HETATM 131 CF BFC A 1 5.487 2.778 -1.309 1.00
> 0.00 C
> HETATM 132 CG BFC A 1 4.591 3.814 -2.015 1.00
> 0.00 C
> HETATM 133 CH BFC A 1 3.801 4.715 -1.053 1.00
> 0.00 C
> HETATM 134 CI BFC A 1 2.988 5.801 -1.771 1.00
> 0.00 C
> HETATM 135 CJ BFC A 1 2.160 6.653 -0.799 1.00
> 0.00 C
> HETATM 136 CK BFC A 1 1.328 7.736 -1.500 1.00
> 0.00 C
> HETATM 137 CL BFC A 1 0.560 8.633 -0.516 1.00
> 0.00 C
> HETATM 138 CM BFC A 1 -0.302 9.699 -1.195 1.00
> 0.00 C
> HETATM 139 HA1 BFC A 1 1.124 -1.605 1.056 1.00
> 0.00 H
> HETATM 140 HA2 BFC A 1 2.392 -0.853 2.076 1.00
> 0.00 H
> HETATM 141 HB BFC A 1 2.141 1.308 0.723 1.00
> 0.00 H
> HETATM 142 HC1 BFC A 1 2.862 -1.163 -0.985 1.00
> 0.00 H
> HETATM 143 HC2 BFC A 1 3.865 -0.642 0.407 1.00
> 0.00 H
> HETATM 144 HD1 BFC A 1 3.187 1.254 -1.912 1.00
> 0.00 H
> HETATM 145 HD2 BFC A 1 4.611 0.159 -1.917 1.00
> 0.00 H
> HETATM 146 HE1 BFC A 1 5.500 1.172 0.131 1.00
> 0.00 H
> HETATM 147 HE2 BFC A 1 4.095 2.266 0.282 1.00
> 0.00 H
> HETATM 148 HF1 BFC A 1 6.091 2.242 -2.076 1.00
> 0.00 H
> HETATM 149 HF2 BFC A 1 6.198 3.330 -0.654 1.00
> 0.00 H
> HETATM 150 HG1 BFC A 1 3.885 3.296 -2.697 1.00
> 0.00 H
> HETATM 151 HG2 BFC A 1 5.246 4.463 -2.639 1.00
> 0.00 H
> HETATM 152 HH1 BFC A 1 4.510 5.203 -0.347 1.00
> 0.00 H
> HETATM 153 HH2 BFC A 1 3.098 4.091 -0.457 1.00
> 0.00 H
> HETATM 154 HI1 BFC A 1 2.301 5.317 -2.498 1.00
> 0.00 H
> HETATM 155 HI2 BFC A 1 3.682 6.462 -2.337 1.00
> 0.00 H
> HETATM 156 HJ1 BFC A 1 2.846 7.138 -0.069 1.00
> 0.00 H
> HETATM 157 HJ2 BFC A 1 1.471 5.988 -0.230 1.00
> 0.00 H
> HETATM 158 HK1 BFC A 1 0.600 7.244 -2.181 1.00
> 0.00 H
> HETATM 159 HK2 BFC A 1 2.004 8.371 -2.115 1.00
> 0.00 H
> HETATM 160 HL1 BFC A 1 1.291 9.135 0.158 1.00
> 0.00 H
> HETATM 161 HL2 BFC A 1 -0.094 7.990 0.114 1.00
> 0.00 H
> HETATM 162 HM1 BFC A 1 0.328 10.382 -1.806 1.00
> 0.00 H
> HETATM 163 HM2 BFC A 1 -0.840 10.303 -0.434 1.00
> 0.00 H
> HETATM 164 HM3 BFC A 1 -1.054 9.220 -1.859 1.00
> 0.00 H
>
> i used g_x2top -f fattyacid.pdb -o out.top -r out.rtp -nopbc command.
> but i got error as
Your model is incomplete. The first carbon has only two bonds, to O and C.
>
> *
> There are 23 name to type translations in file oplsaa.ff
> Generating bonds from distances...
> atom 42
> Can not find forcefield for atom C-1 with 2 bonds
>
> -------------------------------------------------------
> Program g_x2top, VERSION 4.5.5
> Source code file: g_x2top.c, line: 206
>
> Fatal error:
> Could only find a forcefield type for 41 out of 42 atoms.*
>
> i dono how to resolve this . can anyone pls tell me how to solve tis.
> i checked my .n2t file also. but i couldnt get the error.
> help me with your answer ...
> thanking you,
>
>
>
>
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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