Advice implementing this restraint
Posted: Wed Apr 25, 2018 5:56 pm
Hi all,
I'm hoping for some advice on how to implement some restraints.
I have a protein with five-fold axial symmetry (ion channel with five subunits). I have a ligand that binds at the interface of two of any of the subunits. I'd like to have restraining walls that go through each subunit, restraining the ligand to a wedge-shape of the cell that includes just one interface. I would apply these walls such that five ligands are restrained to five of the interfaces in a single simulation.
Is there a way, in OpenMM, to restrain the angle around the z axis, for instance? This would be more elegant than xyz restraints in that it reduces the total number of restraints and thus has better performance. If not then I will look at PLUMED!
cheers for your thoughts
Lewis
I'm hoping for some advice on how to implement some restraints.
I have a protein with five-fold axial symmetry (ion channel with five subunits). I have a ligand that binds at the interface of two of any of the subunits. I'd like to have restraining walls that go through each subunit, restraining the ligand to a wedge-shape of the cell that includes just one interface. I would apply these walls such that five ligands are restrained to five of the interfaces in a single simulation.
Is there a way, in OpenMM, to restrain the angle around the z axis, for instance? This would be more elegant than xyz restraints in that it reduces the total number of restraints and thus has better performance. If not then I will look at PLUMED!
cheers for your thoughts
Lewis