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?
Mohsin Yousuf Lone
Dear Malathi,
Please go through the GROMACS Tutorial by Justin A. Lemkul, Ph.D.
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Anu Manhas
What force field you are using and what type of error are you getting? Is it related to het atom?
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Alex Rayevsky
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?
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