Example 20: Mitochondrial methylmalonyl-CoA mutase (Alphafold P22033)¶

Alphafold ID P22033 is a predicted structure of the mitochondrial methylmalonyl-CoA mutase, a key enzyme in the metabolism of certain amino acids and fatty acids. This example demonstrates how to use Pestifer to set up a simulation environment for this protein.

# Author: Cameron F. Abrams <cfa22@drexel.edu>

title: Mitochondrial methylmalonyl-CoA mutase (Alphafold P22033)
tasks:
- fetch:
    sourceID: P22033
    source: alphafold
- psfgen:
- validate:
    tests:
      - residue_test:
          name: 750 residues present
          selection: protein
          measure: residue_count
          value: 750
- md:
    ensemble: minimize
- pdb2pqr:
    pH: 7.0
- validate:
    tests:
      - residue_test:
          name: protonated ASP
          selection: protein and chain A and resid 156 165 283 437 and name HD2
          measure: atom_count
          value: 4
      - residue_test:
          name: protonated GLU
          selection: protein and chain A and resid 65 276 373 392 and name HE2
          measure: atom_count
          value: 4
- solvate:
    salt_con: 0.15
- md:
    ensemble: minimize
- md:
    ensemble: nvt
    nsteps: 1000
- md:
    ensemble: npt
    nsteps: 1000
- md:
    ensemble: npt
    nsteps: 10000
- mdplot:
    basename: solvated
    timeseries:
      - density
    grid: True
- terminate:
    basename: my_mcm
    artifacts: artifacts
    package:
      basename: my_mcm
      namd:
        ensemble: npt
        nsteps: 1000000
        firsttimestep: 0

Pipeline task summary¶
Step	Task	Details
1	`fetch`	AlphaFold model, UniProt P22033
2	`psfgen`	standard build
3	`validate`	1 test(s)
4	`md`	minimize
5	`pdb2pqr`	protonate at pH 7.0
6	`validate`	2 test(s)
7	`solvate`	water box + 0.15 M salt
8	`md`	minimize → nvt (1,000 steps) → npt (11,000 steps, 2 phases)
9	`mdplot`	equilibration time-series plots → `mdplots/`
10	`terminate`	basename: `my_mcm`; package: `my_mcm`