[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

[ZHANG Cheng]

Dear Gromacs,
I got this fatal error after running "pdb2gmx":


Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.



However, the residue 1 in the PDB is:


ATOM      1  N   ASP L   1      24.330  14.711  -3.854  1.00  0.00           N  
ATOM      2  CA  ASP L   1      25.669  15.093  -3.310  1.00  0.00           C  
ATOM      3  C   ASP L   1      25.766  14.899  -1.791  1.00  0.00           C  
ATOM      4  O   ASP L   1      26.581  14.101  -1.318  1.00  0.00           O  
ATOM      5  CB  ASP L   1      25.989  16.552  -3.646  1.00  0.00           C  
ATOM      6  CG  ASP L   1      26.260  16.773  -5.128  1.00  0.00           C  
ATOM      7  OD1 ASP L   1      26.489  15.809  -5.821  1.00  0.00           O  
ATOM      8  OD2 ASP L   1      26.236  17.903  -5.554  1.00  0.00           O  
ATOM      9 1H   ASP L   1      24.318  14.855  -4.844  1.00  0.00           H  
ATOM     10 2H   ASP L   1      24.152  13.747  -3.656  1.00  0.00           H  
ATOM     11 3H   ASP L   1      23.623  15.275  -3.427  1.00  0.00           H  
ATOM     12  HA  ASP L   1      26.425  14.456  -3.771  1.00  0.00           H  
ATOM     13 1HB  ASP L   1      25.154  17.186  -3.346  1.00  0.00           H  
ATOM     14 2HB  ASP L   1      26.864  16.873  -3.080  1.00  0.00           H 



You can see that the first atom is just atom N, not missing. Can I ask why I still got this error?


Another mutant file of the protein works totally fine for pdb2gmx. Its 1st residue ASP is the below, I could not see any big difference except slight difference in the coordinates.


ATOM      1  N   ASP L   1      24.330  14.711  -3.854  1.00  0.00           N  
ATOM      2  CA  ASP L   1      25.669  15.093  -3.310  1.00  0.00           C  
ATOM      3  C   ASP L   1      25.766  14.899  -1.791  1.00  0.00           C  
ATOM      4  O   ASP L   1      26.586  14.106  -1.317  1.00  0.00           O  
ATOM      5  CB  ASP L   1      25.989  16.552  -3.646  1.00  0.00           C  
ATOM      6  CG  ASP L   1      26.260  16.773  -5.128  1.00  0.00           C  
ATOM      7  OD1 ASP L   1      26.489  15.810  -5.821  1.00  0.00           O  
ATOM      8  OD2 ASP L   1      26.235  17.904  -5.554  1.00  0.00           O  
ATOM      9 1H   ASP L   1      24.318  14.855  -4.844  1.00  0.00           H  
ATOM     10 2H   ASP L   1      24.152  13.747  -3.656  1.00  0.00           H  
ATOM     11 3H   ASP L   1      23.623  15.275  -3.427  1.00  0.00           H  
ATOM     12  HA  ASP L   1      26.425  14.456  -3.771  1.00  0.00           H  
ATOM     13 1HB  ASP L   1      25.154  17.186  -3.345  1.00  0.00           H  
ATOM     14 2HB  ASP L   1      26.864  16.872  -3.080  1.00  0.00           H


Thank you.


Yours sincerely
Cheng