I am performing a molecular dynamics simulation of hemoglobin using the GROMOS54a7 force field, as it generates topology parameters for the heme group. While most of the steps in my workflow run successfully, I encounter errors during the final gmx mdrun step. The specific issues I am facing are as follows:
Bonds are rotated more than 30 degrees.
Water molecules cannot be settled.
Error messages suggesting bad contacts.
Warnings about wrong PDB files with previous and current coordinates.
Additionally, when I visualize the nvt.gro and npt.gro files in PyMOL, I observe that the Fe atom in the heme group is displaced from its center.
To help diagnose the problem, I am attaching:
A screenshot of the error messages from the mdrun step.
It seems like the system is unstable. You might need to run the equilibrations longer. I assume you restrain the Fe atom as well during the NVT equilibration, right? You might need to run two separate NPT equilibrations - first with restraints and then one without.
also I am currently facing difficulties generating topology parameters for a heme group containing Fe²⁺ at the center. I have attempted to use external tools such as CHARMM and AMBER for topology generation, but I encountered compatibility issues with the Fe atom. Additionally, I have submitted the molecule to the ATB server for GROMOS topology generation, but the job is still in the queue and has not yet been processed.
Could you kindly assist me with this issue or provide a topology file for the heme group with Fe²⁺ at the center? Any help or guidance would be greatly appreciated.
