Example 21: Asymmetric GroEL/GroES Chaperonin Complex¶

PDB ID 1aon is the famous structure of the asymmetric GroEL/GroES chaperonin complex with ADP bound. This build represents Pestifer’s ability to handle ligands like ADP.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
title: Asymmetric GroEL/GroES Chaperonin Complex
tasks:
- fetch:
    sourceID: 1aon
- psfgen:
    source:
      biological_assembly: 1
- validate:
    tests:
    - residue_test:
        name: ADPs are present
        selection: resname ADP
        measure: residue_count
        value: 7
- md:
    ensemble: minimize
- solvate:
    salt_con: 0.15
- 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_1aon
    artifacts: artifacts
    package:
      basename: my_1aon
      namd:
        ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 1AON
2	`psfgen`	standard build
3	`validate`	1 test(s)
4	`md`	minimize
5	`solvate`	water box + 0.15 M salt
6	`md`	minimize → NVT (2,000 steps) → NPT (16,200 steps, 5 phases)
7	`mdplot`	equilibration time-series plots → `mdplots/`
8	`terminate`	basename: `my_1aon`; package: `my_1aon`

../../_images/1aon.png — The GroEL/GroES chaperonin complex with ADP bound, in TIP3P water, as built by Pestifer. This system has 550,812 atoms and its box dimensions are 158.5 x 160.3 x 210.9 Å.¶

Reference¶

The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Xu, Z., Horwich, A.L., Sigler, P.B. (1997) Nature 388: 741-750