GROMACS version: 2023
GROMACS modification: Yes
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Recently, I want to make the simulation of a metalloenzyme with ligand. The metalloenzyme has two Mn ions in its active site. When producing the topol file for this metalloenzyme, gromacs cannot find the Mn ion in the rtp file. I have tried many methods. The one is i change the residue name of Mn in the pdb file to Zn, then the topool file of metalloenzyme was produced well using the Gromos 53a6 forcefield. Then i used the ATB server to produce the topol file for the ligand. However, when conducted the gmx genion, it cannot pass.
How can I make a suitable topol file for the metalloenzyme and ligand?
Thanks.