Preparation of Ligand.itp file for a Iron metal coordination complex

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GROMACS version:2020
GROMACS modification: Yes/No
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Dear All,
I am a new user of Gromacs and trying to perform MD simulation of a Protein-Ligand complex (Ligand is a positively charged Iron metal coordination complex). My ligand contains ‘FE’ metal ions which is having coordination number of 6 and already fullfilled by ligand moieties. So I am not expecting any direct metal (FE)-receptor bond or interaction. I have successfully prepared (according to me) the Receptor.gro, ligand.gro, complex.gro and solv.gro using amber14sb_OL15.ff. But after this, when I am trying to prepare the ions.trp, Gromacs is showing the following error-

Fatal error:
Syntax error - File UNL_GMX.itp, line 3
Last line read:
‘[ atomtypes ]’
Invalid order for directive atomtypes

So I have gone through few of the relatable user discussions and understood that may be ‘new atom types’ for Iron (FE) is creating the issue but I am not sure about it. According to the Ptotein-Ligand tutorial, we should introduce the ligand.prm file before the ’ Molecule Types’. But for the AMBER forcefield, there is no ligand.prm generated by [acpype]. In this circumtancees, I have few quires which is listed below,

(1) It seems from the atomtypes.atp that ‘FE’ is already there. But How we can incorporate the value of sigma and epsilon parameters in ffnonbonded.itp?
(2) As Iron (FE) atom will not be in direct contact with receptor , what kind of changes we have to make in the ffbonded.itp.
(3) Is there anything we have to define in the topol.top file before ‘Molecular Types’

Any suggestions would be highly appreciated in this matter. Thanks in advance.

Best Regards
Apurba

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It’s mostly a question of placing the included .itp correctly. In short, all FF information has to be defined before [ moleculetype ]s, and [defaults ] has to be defined only once at the very beginning.

If you know what sigma and epsilon should be, and the atomtype is not defined in your [ atomtypes ], just create an entry by analogy. You can copy the .ff directory from Gromacs files to your working directory, or make a self-contained .top file and edit it directly. If you don’t have any bonded terms to your iron ion, that would be it.

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Thanks for your reply. I will follow the instruction and get back to you.