I merged heme and a ligand by manually editing gro and top instead of “-merge”, after which MD was performed. This result was unexpected for me because heme is not covalent binding to the protein, and it and the ligand are separated from the protein in less than 10ns of MD, but the ligand can only be injected once, so how do I make sure that the protein and heme are integrated as a whole, and MD of the ligand with the conjugated protein I constructed?
i think instead of injecting the ligand at gro file making, you can use the complex after performing the molecular docking and then make the gro file. and to make sure the ligand is still attached to heme, there are commands to extract the complex at anytime of simulation. by which you can visualize.
Kavita Patel yes, I try it in CHARMM-GUI, but I can't generate a complex model of .gro, because no CYS-HEME option for me to chooes
And we also require the force field for metalloproteins that is compatible with small molecules.
You can certainly go ahead with the Desmond. For Mettaloproteases in Desmond before going for the energy minimization its always suggested to go for the Hetero state generation (Generate Het states) in the preparation step (Which is a part of maestro's Protein Preparation wizard). This step will enables the formation of suitable het state or co-ordinate covalent state in complex with protein, so that your force field like OPLS or CHARMM can easily recognize the metal atom.
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