GROMACS version: 2024.5
GROMACS modification: No
Hi everyone,
I have been trying to simulate a metal complex with a DNA fragment. Starting off, I parametrized the metal complex with easyPARM, a tool to parametrize metal complexes. From easyPARM, I generated prmtop and inpcrd files for the GAFF forcefield, and converted them to GROMACS format using acpype. I created the gro file for the DNA fragment using AMBERFF14SB forcefield, and created a complex.gro file for the DNA-ligand complex. I included the itp for my ligand after the forcefield in the topology file. The system shows no error when I solvate, but when I use grompp to generate a tpr file for the ions, there is a discrepancy of exactly the number of atoms in my ligand in the solv.gro file. I am out of my depth and cant understand where I am going wrong. Please help me
Anurag