[gmx-users] pdb2gmx error

[bharat gupta]

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