[gmx-users] Protein simulation including ligand with Fe(III)

Nikolaos Michelarakis nm884 at york.ac.uk
Wed Aug 6 16:26:57 CEST 2014

Hello again,

Since I could not find any reliable parameters for the Fe-O for the GROMOS
96 forcefield I decided to modify it to use the parameters for its Fe-N in
its HEME group. While reading through the gromos54a7 files i saw that it
has parameters for the Fe-O bond so I thought that it might be able to deal
with my molecule. I run pdb2gmx on my molecule, which included the protein
and the iron, and a topology was produced, giving no errors. However, when
I opened the topology, there is no Fe present in it. Sorry if that's a
silly question but shouldn't it be in there? I can include the files if

Thanks again.


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