Energy min grompp

GROMACS version: 2022
GROMACS modification: No
I have been having trouble building my simulation after several tries.
I have assembled my topology and .gro with a complete model
when I run:
gmx grompp -f em.mdp -c solv_ions.gro -p -o em.tpr

The largest distance between excluded atoms is 1.421 nm, which is larger
than the cut-off distance. This will lead to missing long-range
corrections in the forces and energies.

I looked through my .gro file and my protein has no gaps. my ligands are correctly represented.
when I search for the distance specified

460SOL HW2 4483 1.444 1.451 1.421
all of the distances beyond the cutoff are waters
How do I address these waters?

Water isn’t the problem; grompp is complaining about intramolecular distances being larger than a cutoff, not the values of coordinates themselves. Build the system without the ligand and see if it complains. If it doesn’t, then the issue is with the ligand (which is most likely) and you can troubleshoot from there.

Thanks for pointing me in the right direction.

I have already successfully completed a simulation without my ligands so I think you’re right.

One last question. I am trying to run simulations with alternative residues. My current plan is to run cgenff to create the topology file for each residue to add to my rtp file in my ff dir. I have ran your through tutorials and just want to know if i can use cgenff to generate residue topologies?

The current CHARMM36 force field covers hundreds of modified residues already, so check and make sure whatever you have isn’t already there and the work done for you. CGenFF has been used recently to parametrize novel residues in biopolymers, so the approach is fine (previously we had recommended against mixing CHARMM+CGenFF in this way, but the quality of CGenFF is such that building residues like this is OK as far as we can determine).

Your insight is greatly appreciated.
Thanks for being so supportive.