GROMACS version: version 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
Context: I am trying to run MD simulations for two protein drug targets from M. tuberculosis.
My first target is Mycothiol S-conjugate amidase. (Uniprot code: P9WJN0) The enzyme is a metalloenzyme, having a Fe2+ ion co-ordinated in the active site, which is important for the reaction mechanism.
My second target is QcrAB, (Cryo EM structure: RCSB PDB - 7E1W: Cryo-EM structure of hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203) This is part of the electron transport chain and the QcrA chain has an Iron-Sulfur Cluster (Fe2S2). The A chain completes the QcrB quinol binding (active) site.
In both cases, I am getting errors at the pdb2gmx step:
Fatal error:
Residue ‘FE’ not found in residue topology database / Residue ‘FES’ not found in residue topology database.
If you have any suggestions / a solution to this, I would be most grateful.
P.S. My background is in biochemistry, not chemistry.
Many thanks