Tazobactam pdb setup

1vm1 TAZ structure	Chemical structure

Without the hydrogens, it is not possible to determine the bond orders and come up with parameters for modeling. There are several possibilities for adding in hydrogens:

• use xleap editor to draw in hydrogens using the published chemical structure showing bond orders.
• use a ligand index such as "Macromolecular Structure Database" (MSD)
• edit in guesses to the H atoms and their positions by hand in the pdb.

Using the MSD:

1. Type in TAZ or taz in the three-letter-code box or type in tazobactam in the molecule name box and click SEARCH button
2. Click TAZ on left side: make sure:
   • Output is "text"
   • Format is "pdb"
   • Library is "ideal"
   • Hydrogens box MUST BE CHECKED!!!!!
3. click Save button
4. navigate your way to the dir where you want to save the file
5. rename filename from cgi.pl to TAZ.pdb and Save

TAZ.pdb

This structure is ready for antechamber to determine parameters necessary for modeling the molecule in Amber. After determining the parameters in antechamber, there is no more need for this pdb file.