In this tutorial, we will build a description of Glutathione S-Transferase with a bound glutathione and substrate BPDE in a solvent box for use in DYNAMO. This requires some “parameterization” that will be shown during the appropriate build stage.
Files needed for this tutorial:
1. Constructing chain A of GST (PDB id: 4PGT)
(requires protein_opls and 4pgta.seq files which are worth examining)
2. Constructing chain B of GST
3. Construct the system file for the Glutathione system bound to chain A
(requires protein-gglu.opls and ggl1.seq)
4. Construct the system file for the Glutathione system bound to chain B
5. Construct the system for the BPDE substrate
(requires bpde.opls and bpde.seq)
6. Construct the system file for the surrounding water
7. Build the dimmer
8. Build the GST-GSH system
9. Build the GST-GSH-BPDE system
10. Build the solvated Enzymatic system.