Construction of a solvated enzyme system and umbrella sampling along a reaction coordinate

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:

enz-construction.tar
4pgt_rxnsim1.f90
4pgt_rxnsim1.sh

1. Constructing chain A of GST (PDB id: 4PGT)

dynamo 4pgta_gen

(requires protein_opls and 4pgta.seq files which are worth examining)

2. Constructing chain B of GST

dynamo 4pgtb_gen

3. Construct the system file for the Glutathione system bound to chain A

dynamo ggl1_gen1

(requires protein-gglu.opls and ggl1.seq)

4. Construct the system file for the Glutathione system bound to chain B

dynamo ggl2_gen1

5. Construct the system for the BPDE substrate

dynamo bpde_gen

(requires bpde.opls and bpde.seq)

6. Construct the system file for the surrounding water

dynamo water_active_gen

7. Build the dimmer

dynamo 4pgt_gen

8. Build the GST-GSH system

dynamo 4pgt_ggl1_gen

dynamo 4pgt_ggl2_gen

9. Build the GST-GSH-BPDE system

dynamo 4pgt_sub_gen

10. Build the solvated Enzymatic system.

dynamo 4pgt_solvated_gen