Modelling a P450 enyzme

Contents:

• Preparing the P450 system
  • Introduction
  • Initial preparation of the system
• The solvation workflow: setup
  • Introduction to the solvation workflow
  • Step 1: Assigning hydrogen atoms and partial charges
  • Step 2: Solvating the system
  • Step 3: Generating a protein structure file
  • Step 4: Neutralisation of the system
• The solvation workflow: equilibration
  • Step 1: NVT ensemble MD
  • Step 2: NPT ensemble MD
  • Step 3: Production MD
  • Relaxed haem version
  • Full length version
  • MD analysis
  • Taking snapshots from any MD trajectory
• Preparing the non-periodic model
  • Cutting a solvent shell
• QM/MM calculations on the P450 enzyme
  • A single-point QM/MM calculation
  • QM/MM geometry optimisation
  • Porting from other workflows
  • To be continued

In this tutorial you will learn how to perform a QM/MM calculation on an enzymatic system using a CHARMM biomolecular forcefield to describe the environment around the active site.

Note

To run all of the examples in this tutorial, your copy of ChemShell needs to be compiled with DL_POLY, DL_FIELD, NAMD, PDB2PQR and CHARMM forcefield support. Please see the installation guide in the manual for further guidance.

The QM/MM example uses GAMESS-UK as the example QM code, but other QM codes may be substituted for this.

Warning

The workflow described in this tutorial is currently only suitable for calculations using CHARMM forcefields. ChemShell also supports calculations using AMBER forcefields, but these follow a different workflow. Please see the DL_POLY manual page for more details.