Protein/water/counterion/NMR tutorial

This section works through in some detail setting up a protein simulation in AMBER. The example is for plastocyanin in water, and contains a number of things that experienced AMBER users know how to do, but which may be far from obvious for others. In particular, there are a number of items that go beyond a simple protein:

1. Plastocyanin contains a metal ion bound to four amino acids, and I also want to modify a methionine residue that is bound to the copper in such a way that it has a different type of sulfur than is found in the standard database.
2. The Brookhaven crystallographic file (1PLC) contains crystallographic waters, which I might want to keep. Only the oxygen positions are provided, so I will need to try to figure out where to put protons.
3. Somewhat unusually, this PDB file has proton positions for the protein, which I would like to keep. However, Brookhaven uses proton names that are different than what NMR spectroscopists use, and I would like to be able to use the latter to make easy contact with NMR results.
4. Using the most probable ionization states of the protein (at neutral pH) results in a protein with a net charge of -8, so I would like to include mobile counterions in the solution to create an overall neutral system.

This will be a lot of work, but it's infinitely easier now in AMBER than it used to be. We will also use this example to show how to set up some constraints, such as might be found in a NMR refinement, and will illustrate how to carry out simulated annealing optimizations.

Table of Contents

• General preparation.
  • Make database file for the modified residues.
  • Do some editing of the PDB file.

• Set up the system without solvent.
  • Use LEaP to set up the required files.
  • Run a simple minimization.
  • Run simulated annealing optimization .

• Setup the system with counterions in a box of water.
  • Solvate the system with LEaP
  • Run solvated molecular dynamics simulation.