Gromacs Parameters:
Version: Gromacs 2024.2
Force Field: charmm36-jul2021
Hello,
We are trying to simulate cyp51 enzyme that contains the heme group, in this case, the iron atom is bonded with a sulfur atom from cysteine residue (CYP434) as a coordinated bound. In a visualization program (ie. Maestro, VMD) the structure 6ux0 (CYP51) contains the coordinate bond between iron (Fe2+) and the sulfur from CYS434. On the other hand, in pdb2gmx we noted that in the .gro file the coordinated bond is broken, the cysteine -SH angle was modified and the coordinated bond is no longer established with iron.
Do you have any suggestions as to how we can conserve the coordinated bond in the next steps?