Example 6: Fasciculin 1 at pH 7.0¶

PDB ID 1fas is the 1.9-Å resolution structure of fasciculin 1, an anti-acetylcholinesterase toxin from green mamba snake venom. This example demonstrates how to use the pdb2pqr task to assign protonation states to ionizable residues at a specified pH. The pdb2pqr task is used to prepare the structure for simulation by assigning appropriate protonation states based on the pH value specified in the YAML configuration file. Here we set the pH to 7.0. We also exclude all atoms with altLocs values of ‘B’.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Fasciculin 1, demonstration of pdb2pqr usage
#
title: Fasciculin 1, an Anti-Acetylcholinesterase Toxin from Green Mamba Snake Venom
tasks:
- fetch:
    sourceID: 1fas
- psfgen:
- md:
    ensemble: minimize
- pdb2pqr:
    pH: 7.0
- validate:
    tests:
      - residue_test:
          name: no altloc B atoms present
          selection: altloc B
          measure: atom_count
          value: 0
- solvate:
    anion: CLA
    cation: SOD
    salt_con: 0.154
- 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
    timeseries:
    - density
- terminate:
    basename: my_1fas
    artifacts: artifacts
    package:
      basename: prod_1fas
      namd:
        ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 1FAS
2	`psfgen`	standard build
3	`md`	minimize
4	`pdb2pqr`	protonate at pH 7.0
5	`validate`	1 test(s)
6	`solvate`	water box + 0.154 M SOD/CLA
7	`md`	minimize → NVT (2,000 steps) → NPT (16,200 steps, 5 phases)
8	`mdplot`	equilibration time-series plots → `mdplots/`
9	`terminate`	basename: `my_1fas`; package: `prod_1fas`

Note that the pdb2pqr task is invoked immediately after the psfgen task but before the solvate task. The pdb2pqr task is documented at pdb2pqr.

../../_images/1fas.png — Fasciculin 1 (PDB ID 1fas).¶

Reference¶

1.9-Å resolution structure of fasciculin 1, an anti-acetylcholinesterase toxin from green mamba snake venom. le Du, M.H., Marchot, P., Bougis, P.E., Fontecilla-Camps, J.C. (1992) J Biological Chem 267: 22122-22130. PDF