[gmx-users] request

[Group Gro]

Dear Gromacs Users.


I apologize for asking a question that has come up several times by numerous users in the previous e-mails, but I have read the answers and suggestions to those posts and I am not still able to solve the problem based on them. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I want to work on "Human Glutathione Peroxidase" and downloaded its pdb file, but when I try pdb2gmx, I face Fatal Error:

Program pdb2gmx, VERSION 4.5.5 
Source code file:
/build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 91 
Fatal error: 
Atom CD is used in an interaction of
type atom in the topology 
database, but an atom of that name was
not found in residue 
number 50. 


I tried different force fields, for example OPLS-AA/L all-atom force field, different versions of AMBERs, but I
always get the same problem! When I tried GROMOS's versions, the problem goes on CZ atom instead of CD. Here is a chunk of my pdb file (I have also attached the full pdb file to this e-mail):

SHEET    6   A 1 PHE A 183  PRO A190  0
SHEET    7   A 1 GLY A 192  HIS A200  0
MODEL
ATOM      1    N GLY A  38      -4.242  -9.833 -26.316  1.00  0.00           N  
ATOM      2   CA GLY A  38      -3.416 -10.949 -25.765  1.00  0.00           C  
ATOM      3    C GLY A  38      -1.953 -10.570 -25.632  1.00  0.00           C  
ATOM      4    O GLY A  38      -1.069
 -11.266 -26.159  1.00  0.00           O  
ATOM      5    N THR A  39      -1.673  -9.461 -24.940  1.00  0.00           N  
ATOM      6   CA THR A  39      -0.286  -9.039 -24.705  1.00  0.00           C  
ATOM      7    C THR A  39      -0.073  -8.722 -23.214  1.00  0.00           C  
ATOM      8    O THR A  39      -1.035  -8.559 -22.442  1.00 
 0.00           O  
ATOM      9   CB THR A  39       0.124  -7.784 -25.533  1.00  0.00           C  
ATOM     10  OG1 THR A  39      -0.415  -6.602 -24.926  1.00  0.00           O  
ATOM     11  CG2 THR A  39      -0.309  -7.882 -27.037  1.00  0.00           C  
…..
ATOM     91  OD1 ASP A  49      10.106   1.841  -5.471  1.00  0.00           O  
ATOM     92  OD2 ASP A  49      12.010   2.918  -5.273  1.00  0.00           O  
ATOM     93    N GLY A   50       8.192   0.495  -3.643  1.00  0.00           N  
ATOM     94   CA GLY A   50       6.805   0.919  -3.449  1.00  0.00           C  
ATOM     95    C GLY A   50       6.525   2.278  -4.054  1.00  0.00           C  
ATOM    
 96    O GLY A   50       5.449   2.818  -3.864  1.00  0.00           O  
ATOM     97    N GLU A   51       7.471   2.832  -4.802  1.00  0.00           N  
ATOM     98   CA GLU A   51       7.351   4.238  -5.211  1.00  0.00           C  
ATOM     99    C GLU A    51       6.737   4.438  -6.592  1.00  0.00           C  
ATOM    100    O GLU A
   51       6.291   5.522  -6.897  1.00  0.00           O  
ATOM    101   CB GLU A  51       8.713   4.941  -5.174  1.00  0.00           C  
ATOM    102   CG GLU A  51       9.283   5.140  -3.759  1.00  0.00           C  
ATOM    103   CD GLU A  51       8.612   6.301  -3.006  1.00  0.00           C  
ATOM    104    N GLU A   52       6.729  
 3.418  -7.432  1.00  0.00           N  
…. 
ATOM    3035    OH TYR  A   228      -9.320
-43.377 -52.577  1.00  0.00           O 
TER    3036      TYR A 228 
ENDMDL 
HETATM 3037   CL  CL 11000     -16.070
-39.525  -6.168  1.00  0.00          CL 
HETATM 3038   NA  NA 11001      -1.679
-34.065  -0.491  1.00  0.00          NA 
CONECT  996 1519 
CONECT 1021 1519 
CONECT 1519  996 1021 
END

I know that the residue number printed
by pdb2gmx is actually starting from zero, so the problem is actually in GLU.
In both rtp file and pdb I have CD atom. Some suggestions wanted to
change the order of C and O in pdb file, but it didn't work. What should I do?
Thanks a lot.
Groupgro.