[gmx-users] pdb2gmx error
Mark Abraham
mark.j.abraham at gmail.com
Thu Jun 16 13:26:27 CEST 2016
Hi,
Why is your residue numbering and residue naming changing in mutually
inconsistent ways?
Mark
On Thu, Jun 16, 2016 at 9:36 AM bharat gupta <bharat.85.monu at gmail.com>
wrote:
> Hi,
>
> I have been trying to build the toplogy for cellopentoase using the newly
> derived parameters mentioned in this paper:
> http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the
> gromacs website:
> http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar
>
> When I try to construct the topology file using this forcefield, I am
> getting the following error:
>
> Fatal error:
> Residue 6 named GLCN of a molecule in the input file was mapped
> to an entry in the topology database, but the atom C1 used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> I have only 5 residues in the pdb file, but gromacs is counting it as 6
> residues. Here's the pdb file:
>
> HEADER CP5
> ATOM 1 O2 GLC0 1 7.400 0.776 35.278 0.70 24.55
> O
> ATOM 2 C2 GLC0 1 6.024 0.721 35.632 0.70 23.65
> C
> ATOM 3 C3 GLC0 1 5.240 0.984 34.354 0.70 21.57
> C
> ATOM 4 O3 GLC0 1 5.144 -0.245 33.608 0.70 14.59
> O
> ATOM 5 C4 GLC0 1 3.902 1.571 34.776 0.70 20.91
> C
> ATOM 6 O4 GLC0 1 3.006 1.662 33.670 0.70 19.67
> O
> ATOM 7 C5 GLC0 1 4.174 2.944 35.391 0.70 22.32
> C
> ATOM 8 C6 GLC0 1 2.914 3.605 35.899 0.70 21.51
> C
> ATOM 9 O6 GLC0 1 2.201 2.690 36.737 0.70 20.09
> O
> ATOM 10 O5 GLC0 1 5.080 2.890 36.510 0.70 24.12
> O
> ATOM 11 C1 GLC0 1 5.742 1.651 36.843 0.70 26.75
> C
> ATOM 12 O1 GLC 1 5.207 0.892 37.971 0.70 30.32
> O
> ATOM 13 C4 GLC 2 4.222 1.340 38.917 0.70 32.87
> C
> ATOM 14 C5 GLC 2 4.753 1.239 40.352 0.70 33.51
> C
> ATOM 15 O5 GLC 2 3.711 1.506 41.306 0.70 35.29
> O
> ATOM 16 C6 GLC 2 5.888 2.194 40.665 0.70 34.02
> C
> ATOM 17 O6 GLC 2 5.803 2.537 42.057 0.70 32.97
> O
> ATOM 18 C3 GLC 2 3.072 0.331 38.851 0.70 33.72
> C
> ATOM 19 O3 GLC 2 2.435 0.360 37.564 0.70 34.01
> O
> ATOM 20 C2 GLC 2 2.027 0.450 39.972 0.70 35.29
> C
> ATOM 21 O2 GLC 2 1.149 -0.684 39.932 0.70 36.32
> O
> ATOM 22 C1 GLC 2 2.684 0.512 41.351 0.70 36.04
> C
> ATOM 23 O1 GLC 2 1.704 0.843 42.349 0.70 36.96
> O
> ATOM 24 C4 GLC 3 2.032 0.454 43.689 0.70 38.12
> C
> ATOM 25 C5 GLC 3 0.810 -0.195 44.344 0.70 38.87
> C
> ATOM 26 O5 GLC 3 1.085 -0.507 45.715 0.70 39.40
> O
> ATOM 27 C6 GLC 3 0.372 -1.455 43.605 0.70 38.87
> C
> ATOM 28 O6 GLC 3 -0.996 -1.300 43.220 0.70 39.09
> O
> ATOM 29 C3 GLC 3 2.455 1.683 44.498 0.70 38.55
> C
> ATOM 30 O3 GLC 3 3.729 2.152 44.043 0.70 38.93
> O
> ATOM 31 C2 GLC 3 2.550 1.405 45.997 0.70 39.25
> C
> ATOM 32 O2 GLC 3 2.700 2.646 46.700 0.70 38.44
> O
> ATOM 33 C1 GLC 3 1.319 0.663 46.514 0.70 39.97
> C
> ATOM 34 O1 GLC 3 1.522 0.333 47.897 0.70 41.30
> O
> ATOM 35 C4 GLC 4 0.320 -0.039 48.583 0.70 42.19
> C
> ATOM 36 C5 GLC 4 -0.067 0.972 49.664 0.70 42.80
> C
> ATOM 37 O5 GLC 4 -1.358 0.617 50.163 0.70 43.08
> O
> ATOM 38 C6 GLC 4 -0.082 2.420 49.189 0.70 43.23
> C
> ATOM 39 O6 GLC 4 -0.900 2.532 48.019 0.70 43.36
> O
> ATOM 40 C3 GLC 4 0.485 -1.387 49.281 0.70 42.24
> C
> ATOM 41 O3 GLC 4 0.818 -2.397 48.323 0.70 41.16
> O
> ATOM 42 C2 GLC 4 -0.782 -1.783 50.046 0.70 42.64
> C
> ATOM 43 O2 GLC 4 -0.470 -2.862 50.935 0.70 42.32
> O
> ATOM 44 C1 GLC 4 -1.375 -0.633 50.870 0.70 43.60
> C
> ATOM 45 O1 GLCN 4 -2.732 -0.947 51.190 0.70 45.14
> O
> ATOM 46 C4 GLCN 5 -3.137 -0.484 52.482 0.70 46.29
> C
> ATOM 47 C3 GLCN 5 -4.035 0.750 52.337 0.70 46.70
> C
> ATOM 48 O3 GLCN 5 -3.269 1.864 51.865 0.70 46.85
> O
> ATOM 49 C2 GLCN 5 -4.706 1.124 53.659 0.70 47.10
> C
> ATOM 50 O2 GLCN 5 -5.680 2.147 53.435 0.70 47.17
> O
> ATOM 51 C1 GLCN 5 -5.377 -0.097 54.282 0.70 47.34
> C
> ATOM 52 O1 GLCN 5 -5.958 0.264 55.539 0.70 47.48
> O
> ATOM 53 O5 GLCN 5 -4.397 -1.126 54.467 0.70 47.17
> O
> ATOM 54 C5 GLCN 5 -3.867 -1.611 53.225 0.70 46.80
> C
> ATOM 55 C6 GLCN 5 -2.967 -2.814 53.497 0.70 46.93
> C
> ATOM 56 O6 GLCN 5 -1.934 -2.454 54.421 0.70 47.39
> O
> END
>
> Can anyone let me know what am I doing wrong?
>
> I am trying to perform MD simulation of protein with cellopentoase. So, in
> order to obtain the parameters for cellopentoase, I am following the
> parameters mentioned above.
>
>
> --
> *Best Regards*
> Bharat
> --
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