I want to do MD simulation for metallo enzyme as well as protein-ligand complex in GROMACS. But when i use the pdb structure with zn ions it showing error. Help me to sort out this problem. Which forcefield should i use? what changes do i need to made in pdb for topology creation?
Dear Malathi,
Please go through the GROMACS Tutorial by Justin A. Lemkul, Ph.D.
What force field you are using and what type of error are you getting? Is it related to het atom?
As I remember You don't need to change anything in topology, just rename aminoacids coordinating metal atom to those with charged states. At least amber/charmm force fields working this way without constraints or something else.. On which step have You got an error?
You can directly perform using the latest Gromos force field. This force field works for most of the metals.
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