HELP!!Read PDB files

[huiling25]

PDBReader reader1 = new PDBReader(new FileReader("M5250.pdb"));
IChemFile content1=(IChemFile)reader1.read((IChemObject)new org.openscience.cdk.ChemFile());
IAtomContainer[] c1 = ChemFileManipulator.getAllAtomContainers(content1);
Fingerprinter fp1 = new Fingerprinter();
BitSet fingerprint1 = fp1.getFingerprint(c1[0]);
System.out.println(fingerprint1);

There is no problem in compiling. However, I got these statements when
executing:
Did not recognize PDB atom type: MOL.C1
Did not recognize PDB atom type: MOL.C2
Did not recognize PDB atom type: MOL.O3
Did not recognize PDB atom type: MOL.N4
Did not recognize PDB atom type: MOL.C5
Did not recognize PDB atom type: MOL.C6
Did not recognize PDB atom type: MOL.C7
Did not recognize PDB atom type: MOL.C8
Did not recognize PDB atom type: MOL.N9
Did not recognize PDB atom type: MOL.H10
Did not recognize PDB atom type: MOL.C11
Did not recognize PDB atom type: MOL.C12
Did not recognize PDB atom type: MOL.C13
Did not recognize PDB atom type: MOL.C14
Did not recognize PDB atom type: MOL.C15
Did not recognize PDB atom type: MOL.C16
Did not recognize PDB atom type: MOL.O17
Did not recognize PDB atom type: MOL.C18
In addtion, the fingeprint is wrong when I printed it out. Is there another simpler way for readin pdb file?