I want to do an MD simulation of a metalloprotein with an organic ligand using gromacs and when use gmx pdb2gmx for the metalloprotein stripped of the ligand i get the following error message;
Fatal error:
The residues in the chain FE1--OH3 do not have a consistent type. The first
residue has type 'Other', while residue OH3 is of type 'Ion'. Either there is
a mistake in your chain, or it includes nonstandard residue names that have
not yet been added to the residuetypes.dat file in the GROMACS library
directory. If there are other molecules such as ligands, they should not have
the same chain ID as the adjacent protein chain since it's a separate
molecule.
I would like someone to advice me on what to do or how to go about generating a topology file for the metalloprotein that i can use on gromacs for the protein-ligand simulation.
I have uploaded the pdb file for the metalloprotein
Olatomide Fadare CHARMM-GUI has many useful tools to generate input files (Top, FF, ...) for different platforms (GROMACS, LAMMPS, CHARMM, ...). Please take a look at the input generator part here: http://www.charmm-gui.org/?doc=input
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