Example 19: Sperm whale myoglobin¶

PDB ID 1mob is one of 16 structures of sperm whale myoglobin mutants determined by the Phillips lab using X-ray crystallography. This example demonstrates that pestifer can handle the heme group and the covalent bond between the heme and the His93 residue. The heme group is a prosthetic group that is not part of the protein sequence, but it is included in the PDB file. Pestifer can handle this by using the psfgen task to generate a PSF file that includes the heme group and the covalent bond.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
#
# High-Resolution Crystal Structures of Distal Histidine Mutants of Sperm Whale Myoglobin
#
# This file was generated using the command ` pestifer new-system --id 1mob --build-type full`
# and subsequently edited.
#
# Notes:
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: my_1mob.tgz

title: Sperm whale myoglobin
tasks:
  - fetch:
      sourceID: 1mob
  - psfgen:
  - validate:
      tests:
        - residue_test:
            name: HEME residue present
            selection: resname HEME
            measure: residue_count
            value: 1
  - 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_1mob
      artifacts: artifacts
      package:
        basename: my_1mob
        namd:
          ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 1MOB
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_1mob`; package: `my_1mob`

1mob structure — Sperm whale myoglobin structure from PDB ID 1mob. The heme group and His93 residue are shown in licorice representation, including the bond between the heme iron and the Nε of His93.¶