[gmx-users] Residue 'DUM' not found in residue topology database

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,

I try to use GROMACS for my protein where I added a layer of dummy atoms
simulating the membrane around it.
But now when I want to call "pdb2gmx" I always get the error:
Fatal error:
Residue 'DUM' not found in residue topology database
I understand the error, that there is no entry for the dummy residue in
the .tpr file. But is there a possibility to add it there. Because the
file don't look like that I can just write "DUM" in it.


my pdb file looks like this:

ATOM   2597  CB  LEU A 313      12.816 -29.877 -23.547  1.00 55.31        
  C
ATOM   2598  CG  LEU A 313      14.261 -29.695 -23.059  1.00 54.06        
  C
ATOM   2599  CD1 LEU A 313      15.169 -30.640 -23.866  1.00 53.26        
  C
ATOM   2600  CD2 LEU A 313      14.757 -28.257 -23.179  1.00 54.46        
  C
TER
HETATM 3076  DUM DUM A 314      -4.000 -49.000   6.000  1.00  1.70
HETATM 3077  DUM DUM A 314      -4.000 -49.000   7.000  1.00  1.70
HETATM 3078  DUM DUM A 314      -4.000 -48.000   6.000  1.00  1.70
HETATM 3079  DUM DUM A 314      -4.000 -48.000   7.000  1.00  1.70
.
.
.
.
HETATM 36213 O   HOH A 527      25.281 -35.299  13.147  1.00 37.03        
  O
HETATM 36214 O   HOH A 528      46.452 -27.955 -20.733  1.00 19.63        
  O
HETATM 36215 O   HOH A 530      32.439 -23.614 -26.720  1.00 27.12        
  O
TER






Best regards,
Eva