I am using AMBER for MD. However I am not able to figure out how to select atoms or residues to apply a harmonic restraint.
I have crystal structure from PDB and and I want run MD simulations on it. At the active site there is a Zinc ion and I want it remain there along with surrounding residues, water molecule and ligand so that it stays there in similar conformation during MD run. I don't want it to fly away. Subsequently I want to run QM simulations on the same systems.
Is there any way to restrain the atoms and residues within a particular distance from specific atom e.g. zinc?
my pdb is 2v5w
You can reparametrize the Zn ion and its surrounding residues to a new bonded model, which could remain the coordination of Zn and its spatial neighbors.
Additional restraints are often inappropriate when treating these systems containing metal centers.
Interesting question! But im not sure, if you restrain the Zn ion in the pocket, what suppose should be the consequences. They wouldnt take part in the dynamics. As other suggested you can go for bonded MD in If you using AMBER.
First, i would apply flat-bottomed distance restraints; it is simple to do and it may serve the purpose.
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