Example 22: Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus¶

PDB ID 2bgj is the structure of ferredoxin-NADP(H) reductase from Rhodobacter capsulatus. This example demonstrates how to build a system with a flavin cofactor (FAD). Because FAD is already handled by the CHARMM36 force field, this is actually pretty easy. This structure also contains four distinct but identical proteins, so we delete all but one of them.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
title: Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus
tasks:
- fetch:
    sourceID: 2bgj
- psfgen:
    source:
      exclude:
        - chainID in ['B', 'C', 'D']  # remove other protein chains
- validate:
    tests:
    - residue_test:
        name: no chains B, C, or D
        selection: protein and chain B C D
        measure: atom_count
        value: 0
    - residue_test:
        name: has FAD
        selection: resname FAD
        measure: residue_count
        value: 1
- md:
    ensemble: minimize
- solvate:
- md:
    ensemble: minimize
- md:
    ensemble: NVT
- md:
    ensemble: NPT
    nsteps: 200
- md:
    ensemble: NPT
    nsteps: 400
- md:
    ensemble: NPT
    nsteps: 800
- md:
    ensemble: NPT
    nsteps: 1600
- md:
    ensemble: NPT
    nsteps: 13200
- mdplot:
    basename: solvated
    grid: true
    timeseries:
    - density
- terminate:
    basename: my_2bgj
    artifacts: artifacts
    package:
      basename: my_2bgj
      namd:
        ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 2BGJ
2	`psfgen`	exclusions
3	`validate`	2 test(s)
4	`md`	minimize
5	`solvate`	water box
6	`md`	minimize → NVT (2,000 steps) → NPT (16,200 steps, 5 phases)
7	`mdplot`	equilibration time-series plots → `mdplots/`
8	`terminate`	basename: `my_2bgj`; package: `my_2bgj`

../../_images/2bgj.png — The ferredoxin-NADP(H) reductase from *Rhodobacter capsulatus*, as built by Pestifer. This system has 32,240 atoms and its box dimensions are 72.2 x 71.2 x 61.3 Å.¶

Reference¶

The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism. Nogues, I., Perez-Dorado, I., Frago, S., Bittel, C., Mayhew, S.G., Gomez-Moreno, C., Hermoso, J.A., Medina, M., Cortez, N., Carrillo, N. (2005) Biochemistry 44: 11730-11740