The amino acids reported as errors by pdb2gmx do not correspond to the amino acids in the structure

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GROMACS version:2025.2
GROMACS modification: No
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Recently, I’ve been simulating proteins containing non-standard amino acids. After constructing the RTP entry, I hastily created a test PDB file to verify the correctness of both the RTP entry and HDB file. This PDB file consists of three amino acids: GLY-LMA-GLY, where LMA represents an edited lysine—the non-standard residue I’m using. However, I encountered the following fatal error:

Fatal error:

Residue 3 named LMA of a molecule in the input file was mapped

to an entry in the topology database, but the atom C used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

In reality, residue 3 is not LMA at all, but GLY. Why does this happen? Thanks for your help.

ATOM      1  N   GLY A   1       0.000   0.000   0.000  1.00  0.00           N  
ATOM      2  CA  GLY A   1       1.447   0.000   0.000  1.00  0.00           C  
ATOM      3  C   GLY A   1       1.968   0.000   1.433  1.00  0.00           C  
ATOM      4  O   GLY A   1       1.239   0.000   2.422  1.00  0.00           O  
ATOM      5  H   GLY A   1      -0.472  -0.003   0.900  1.00  0.00           H  
ATOM      6  HN  GLY A   1      -0.508   0.077  -0.877  1.00  0.00           H  
ATOM      7  HA1 GLY A   1       1.799  -0.896  -0.522  1.00  0.00           H  
ATOM      8  HA2 GLY A   1       1.800   0.893  -0.524  1.00  0.00           H  
ATOM      9  N1  LMA A   2       3.288  -0.000   1.666  1.00  0.00           N  
ATOM     10  C3  LMA A   2       3.787   0.000   3.038  1.00  0.00           C  
ATOM     11  C6  LMA A   2       5.321   0.000   2.940  1.00  0.00           C  
ATOM     12  O10 LMA A   2       5.928  -0.000   1.870  1.00  0.00           O  
ATOM     13  C5  LMA A   2       3.256  -1.222   3.800  1.00  0.00           C  
ATOM     14  C9  LMA A   2       3.621  -1.231   5.287  1.00  0.00           C  
ATOM     15  C13 LMA A   2       2.911  -2.369   6.026  1.00  0.00           C  
ATOM     16  C16 LMA A   2       3.346  -2.436   7.489  1.00  0.00           C  
ATOM     17  N19 LMA A   2       2.634  -3.502   8.181  1.00  0.00           N  
ATOM     18  C31 LMA A   2       3.133  -3.615   9.559  1.00  0.00           C  
ATOM     19  O32 LMA A   2       2.373  -3.532  10.494  1.00  0.00           O  
ATOM     20  C21 LMA A   2       4.636  -3.839   9.813  1.00  0.00           C  
ATOM     21  C23 LMA A   2       4.840  -4.390  11.236  1.00  0.00           C  
ATOM     22  C27 LMA A   2       5.385  -2.502   9.668  1.00  0.00           C  
ATOM     23  H01 LMA A   2       5.024  -4.553   9.086  1.00  0.00           H  
ATOM     24  H02 LMA A   2       1.908  -4.076   7.776  1.00  0.00           H  
ATOM     25  H03 LMA A   2       5.223  -5.409  11.180  1.00  0.00           H  
ATOM     26  H04 LMA A   2       5.550  -2.069  10.655  1.00  0.00           H  
ATOM     27  H05 LMA A   2       3.888  -4.388  11.767  1.00  0.00           H  
ATOM     28  H06 LMA A   2       5.555  -3.763  11.769  1.00  0.00           H  
ATOM     29  H07 LMA A   2       4.792  -1.815   9.065  1.00  0.00           H  
ATOM     30  H08 LMA A   2       6.346  -2.674   9.183  1.00  0.00           H  
ATOM     31  H   LMA A   2       3.889  -0.403   0.953  1.00  0.00           H  
ATOM     32  HA  LMA A   2       3.456   0.927   3.522  1.00  0.00           H  
ATOM     33  HB1 LMA A   2       3.632  -2.142   3.333  1.00  0.00           H  
ATOM     34  HB2 LMA A   2       2.163  -1.254   3.704  1.00  0.00           H  
ATOM     35  HG1 LMA A   2       3.347  -0.272   5.744  1.00  0.00           H  
ATOM     36  HG2 LMA A   2       4.704  -1.353   5.403  1.00  0.00           H  
ATOM     37  HD1 LMA A   2       3.133  -3.323   5.529  1.00  0.00           H  
ATOM     38  HD2 LMA A   2       1.826  -2.219   5.966  1.00  0.00           H  
ATOM     39  HE1 LMA A   2       3.139  -1.484   7.989  1.00  0.00           H  
ATOM     40  HE2 LMA A   2       4.424  -2.619   7.554  1.00  0.00           H  
ATOM     41  N   GLY A   3       6.064   0.000   4.055  1.00  0.00           N  
ATOM     42  CA  GLY A   3       7.508   0.000   3.963  1.00  0.00           C  
ATOM     43  C   GLY A   3       8.120   0.000   5.360  1.00  0.00           C  
ATOM     44  O   GLY A   3       7.454   0.001   6.393  1.00  0.00           O  
ATOM     45  OXT GLY A   3       9.469   0.000   5.426  1.00  0.00           O  
ATOM     46  H   GLY A   3       5.650  -0.002   4.983  1.00  0.00           H  
ATOM     47  HA1 GLY A   3       7.826  -0.896   3.420  1.00  0.00           H  
ATOM     48  HA2 GLY A   3       7.827   0.893   3.418  1.00  0.00           H  
ATOM     49  HO  GLY A   3      10.045  -0.000   4.531  1.00  0.00           H  
TER
END

LMArtp.txt (17.9 KB)

LMAhdb.txt (475 Bytes)

2

Did you define LMA in residuetypes.dat as a protein residue? If not, likely pdb2gmx has warned you that it is detecting dissimilar residue types in the chain and is trying to patch LMA like it would any other C-terminal residue by looking for a carboxylate C atom. The other possibility is that the GLY residue has a bond defined as N -C, meaning it is expecting a typical backbone naming convention to assign bonds. With nonstandard amino acids, it is always best to make sure the backbone atoms are named conventionally to avoid these issues.