[gmx-users] error using pdb2gmx

[Irem Altan]

Hi,

I have a .pdb file that I generated by creating three more copies of the protein according to its P212121 symmetry. I am now trying to run pdb2gmx on it, but I get the following error:

Fatal error:
Residue 111 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

What is weird is that there is no residue 111 that is a cysteine (residue 111 is a phenylalanine). I had run MD simulations successfully on a single copy of this protein before. pdb2gmx runs without an error when I use the old .pdb file. What could be the problem?

Best,
Irem