Example 13: DES-PHE B1 Bovine Insulin Hexamer¶

PDB ID: 2ins is a structure of the bovine insulin hexamer with the DES-PHE B1 mutation. This example demonstrates how to build a system with a hexameric assembly, and it also illustrates how Pestifer automatically handles rare bonds, like the HIS-Nε-Zn bonds in this structure.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Simple build of solvated hexameric insulin 2ins
#
# Notes:
#   - All waters are removed from the input PDB file
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: prod_2ins.tgz
#
title: hexameric insulin
tasks:
  - fetch:
      sourceID: 2ins
      source_format: pdb
  - psfgen:
      source:
        biological_assembly: 1
        exclude:
          - resname == 'HOH'
  - md:
      cpu-override: True
      ensemble: minimize
  - validate:
      tests:
        - residue_test:
            name: no waters
            selection: resname HOH
            measure: residue_count
            value: 0
        - connection_test:
            name: check his-zinc ligation
            selection: (protein and chain B D H P N J and resid 10) or (chain E F K L Q R and resid 1 31)
            connection_type: interresidue
            connection_count: 6
  - 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
      basename: solvated
      grid: True
  - terminate:
      basename: my_2ins
      artifacts: artifacts
      package:
        basename: prod_2ins
        namd:
          ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 2INS
2	`psfgen`	exclusions
3	`md`	minimize
4	`validate`	2 test(s)
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_2ins`; package: `prod_2ins`

Insulin Hexamer — Insulin hexamer (PDB ID 2ins) with zinc ions shown as yellow spheres and the six histidines that coordinate them shown in stick representation.¶

Incidentally, the CHARMMFF patches for creating bonds between histidines and zinc ions are defined in the stream file toppar_all36_prot_modify_res.str, but they are misnamed. In the original file, they appear as:

PRES ZNHD         0.00 ! patch to covalently link HSD to Zn
                       ! Patch is 1-HSD and 2-Zn
BOND 1NE2 2ZN

PRES ZNHE         0.00 ! patch to covalently link HSE to Zn
                       ! Patch is 1-Hse and 2-Zn
BOND 1ND1 2ZN

Clearly, these definitions are backwards. The patch ZNHE should link HSE to Zn, and the patch ZNHD should link HSD to Zn. Pestifer automatically corrects this error on-the-fly when it processes the stream file, so no user intervention is needed.