[gmx-users] missing atom in .rpb: fatal error in pdb2gmx

[Una Bjarnadottir]

Dear Users,

When running pdb2gmx I get this error:

Program pdb2gmx, VERSION 3.3.1
Source code file: add_par.c, line: 221
Fatal error:
Atom NZ1 not found in rtp database in residue LYSH, it looks a bit like NZ

Dr. David van der Spoel already suggested to rename the atom in the pdb 
file which I did and than the same and than this error occured:

Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2gmx.c, line: 393
Fatal error:
Atom NZ1 in residue LYSH 2 not found in rtp entry with 13 atoms while 
sorting atoms

I changed the the NZ atoms in the .rtp file to NZ1 and than this came:
Program pdb2gmx, VERSION 3.3.1
Source code file: add_par.c, line: 221
Fatal error:
Atom NZ2 not found in rtp database in residue LYSH, it looks a bit like NZ1.

I don't understand the problem because in the beginning there was no 
atom called NZ1 in the .pdb file or the .rdb file and than why is 
pdb2gmx complaining about this atom in the first place?

Thanks in advance, replys are highly appreciated.

Una Bjarnadottir