Getting pdb files for input structures

Beta-lactamase search in the pdb database produces 219 matches. Searching for "tazobactam" results in 5 matches. The entry in the pdb database for this tutorial is 1VM1. Retrieve the full text pdb entry to your beta-lactamase tutorial working directory. This pdb file contains several molecules that were part of the crystal structure. We will use only the ones that are specifically related to a molecule of tazobactam bound to the active site of this beta-lactamase. Much of the information that will help in making the decisions about what to keep and what to throw away is in the header of the pdb, so keep the original pdb file around for reference. The pdb contains: We need three parts of the pdb in three separate files at the beginning: beta-lactamase, TAZ, and TBE. Make three copies of the pdb file: vm1_prot.pdb, vm1_taz.pdb, and vm1_tbe.pdb. Edit each to contain only the molecule that each is named after.

Make two separate subdirs to treat each of the protein and TAZ setup:

Now set up the molecules for simulation with sander:
Prepare pdb files for the setup utilities.