Issues with MD Run and Fe Displacement in Hemoglobin Simulation

akanksha_bhosale
Sat, 23 Nov 2024 07:02:44 +0000
User discussions

GROMACS version:2022
GROMACS modification: Yes/No

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:

1. Bonds are rotated more than 30 degrees.

2. Water molecules cannot be settled.

3. Error messages suggesting bad contacts.

4. 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.

5 posts - 2 participants