[gmx-users] Atom -C not found in residue MET1 while adding hydrogens

[Anirban Ghosh]

Hi ALL,

I have a protein pdb file generated using MODELLER. When I use the pdb2gmx command on it, it throws the error:

Atom -C not found in residue MET1 while adding hydrogens
and
Atom OXT in residue LEU 404

The initial and end of the pdb file is like this:
---------------------------------------------------------------------------------
CRYST1  116.083  116.083  116.083  90.00  90.00  90.00 P 1           1
ATOM      1  N   MET X   1      67.960  51.279  76.751  1.00  0.00            
ATOM      2  CA  MET X   1      67.510  49.899  76.451  1.00  0.00            
ATOM      3  CB  MET X   1      65.990  49.769  76.661  1.00  0.00            
ATOM      4  CG  MET X   1      65.570  49.959  78.111  1.00  0.00            
ATOM      5  SD  MET X   1      63.780  49.819  78.401  1.00  0.00            
ATOM      6  CE  MET X   1      63.370  51.379  77.561  1.00  0.00            
ATOM      7  C   MET X   1      67.840  49.539  75.041  1.00  0.00            
ATOM      8  O   MET X   1      68.870  49.949  74.511  1.00  0.00            
ATOM      9  N   ALA X   2      66.970  48.749  74.401  1.00  0.00            
ATOM     10  CA  ALA X   2      67.240  48.349  73.051  1.00  0.00            
ATOM     11  CB  ALA X   2      66.160  47.429  72.461  1.00  0.00            
ATOM     12  C   ALA X   2      67.290  49.579  72.221  1.00  0.00  
.
.
.
ATOM   3069  OD2 ASP X 403      43.890  88.349  36.411  1.00  0.00            
ATOM   3070  C   ASP X 403      42.590  84.299  34.251  1.00  0.00            
ATOM   3071  O   ASP X 403      41.820  84.059  33.321  1.00  0.00            
ATOM   3072  N   LEU X 404      42.790  83.449  35.281  1.00  0.00            
ATOM   3073  CA  LEU X 404      42.100  82.199  35.401  1.00  0.00            
ATOM   3074  CB  LEU X 404      42.250  81.559  36.791  1.00  0.00            
ATOM   3075  CG  LEU X 404      43.710  81.209  37.151  1.00  0.00            
ATOM   3076  CD1 LEU X 404      44.580  82.469  37.241  1.00  0.00            
ATOM   3077  CD2 LEU X 404      43.770  80.349  38.431  1.00  0.00            
ATOM   3078  C   LEU X 404      40.610  82.469  35.201  1.00  0.00            
ATOM   3079  O   LEU X 404      40.010  81.799  34.311  1.00  0.00            
ATOM   3080  OXT LEU X 404      40.050  83.329  35.931  1.00  0.00
END
--------------------------------------------------------------------------------------

How can I remove these errors? Do I need to modify the pdb file anyway?
Any suggestion is welcome.

Regards,

 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India



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