GROMACS version: 2020.7
Hello All,
Would greatly appreciate if you could advice on this, The metalloprotein structure has two identical monomer chains (with 4 Zinc atoms) attached to nucleic acid (DNA scaffold).
Using the traditional GROMACS tutorial, while preparing the protein topology, a roadblock was encountered. The module pdb2gmx, which is used to convert the PDB file into a GROMACS-specific molecular geometry file format (.gro), the topology file (.top) and position restraint file (.itp). This execution kept on failing because this command is only used on systems (pdb file) that only contain residue atoms, not HEATMs. In my case, the Zinc atoms are treated as ligands, hence explains why the execution was unsuccessful.
So i used CharmmGUI to generate input files from x-ray structure(PDB ID:1R4I) and prepped using GUI website, i conducted analysis of the protein which seems to be stable on rmsd,
The goal is to create somewhat reasonable protein topology for zinc metalloprotein and then create ligand topology.
Any recomendation on potentail use of special parametres for zinc metalloprotein using GROMACS.