[gmx-users] pdb2gmx error

[RJ]

Dear gmx,


I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even cleaned my crystal structure using Discovery studio/swissviewer which shows no error on it. I wonder, how do i rectify this problem ? 


WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.


WARNING: WARNING: Residue 366 named LEU of a molecule in the input file was mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.


Before cleaning: 7060 pairs


Residue 32681 named GLN of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.