Example 4: BPTI with a Mutated-in Disulfide Bond¶

Using the mods subdirective, one can introduce new disulfides into an existing structure. This example introduces a disulfide linking residues 11 and 34.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Simple build of solvated BPTI 
#
# Notes:
#   - The phospate ion is excluded
#   - All crystal waters are retained
#   - A new disulfide is introduced via mutation
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: prod_6pti.tgz
#
title: BPTI, no phosphate, introducing a disulfide via mutations
tasks:
  - fetch:
      sourceID: 6pti
  - psfgen:
      source:
        exclude:
          - resname == 'PO4'
      mods:
        mutations:
          - A:T11C
          - A:V34C
        ssbonds:
          - A_11-A_34
  - validate:
      tests:
        - attribute_test:
            name: point mutation
            selection: protein and chain A and resid 11 and name CA
            attribute: resname
            value: CYS
        - attribute_test:
            name: point mutation
            selection: protein and chain A and resid 34 and name CA
            attribute: resname
            value: CYS
        - connection_test:
            name: new disulfide
            selection: protein and chain A and resid 11 34
            connection_type: disulfide
        - residue_test:
            name: phosphate ion excluded
            selection: resname PO4
            measure: residue_count
            value: 0
  - 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:
      timeseries:
        - density
        - - a_x
          - b_y
          - c_z
      basename: solvated
      grid: True
  - terminate:
      basename: my_6pti
      artifacts: artifacts
      package:
        basename: prod_6pti
        namd:
          ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 6PTI
2	`psfgen`	exclusions, mutations, new disulfides
3	`validate`	4 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_6pti`; package: `prod_6pti`

Note that this required first mutating the residues at positions 11 and 34 to cysteines, and then introducing the disulfide mod.