[gmx-users] pdb2gmx fatal error

[Marco Gerolin]

Hello,
I know that is an already know problem but I don't know how to move on.

running pdb2gmx I had this message

Fatal error:
Atom CG is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 163.

Residue 163 is a GLY and has no a CG atom, here it is

ATOM   1244  N   GLY A 163     -81.506  20.445 -34.642  1.00 40.80
  N
ATOM   1245  CA  GLY A 163     -80.353  20.498 -33.724  1.00 39.79
  C
ATOM   1246  C   GLY A 163     -79.161  19.700 -34.239  1.00 38.24
  C
ATOM   1247  O   GLY A 163     -78.044  19.744 -33.659  1.00 40.13
  O


This structure starts from 0 numbering residues, I had the same structure
starting from -1, the error is the same, but now residue 163 is a GLN, here
it is

ATOM   1248  N   GLN A 163     -79.370  19.001 -35.352  1.00 35.72
  N
ATOM   1249  CA  GLN A 163     -78.318  18.161 -35.917  1.00 30.51
  C
ATOM   1250  C   GLN A 163     -77.517  18.844 -37.005  1.00 30.20
  C
ATOM   1251  O   GLN A 163     -78.027  19.724 -37.705  1.00 31.08
  O
ATOM   1252  CB  GLN A 163     -78.886  16.891 -36.484  1.00 30.01
  C
ATOM   1253  CG  GLN A 163     -79.580  16.003 -35.488  1.00 33.24
  C
ATOM   1254  CD  GLN A 163     -79.783  14.619 -36.055  1.00 36.41
  C
ATOM   1255  NE2 GLN A 163     -79.630  13.601 -35.211  1.00 44.58
  N
ATOM   1256  OE1 GLN A 163     -80.100  14.464 -37.234  1.00 44.13
  O

I have tried both with OPLS-AA/L all-atom and CHARMM27 all-atom (with CMAP)
- version 2.0 force fields, but the problem is still the same.

Can anyone help me?

Thanks