#!/usr/bin/env python
"""
PROTEIN SIMULATION
Atomistic protein in water.
"""
from amx import *
init()
make_step(settings.step)
write_mdp()
if state.pdb_source: get_pdb(state.pdb_source)
else: get_start_structure(state.start_structure)
remove_hetero_atoms(
structure='start-structure.pdb',
out='start-structure-trim.pdb')
gmx('pdb2gmx',
base='vacuum',
structure='start-structure-trim.pdb',
gro='vacuum-alone',
water=settings.water,
ff=settings.force_field,
log='pdb2gmx')
copy_file('system.top','vacuum.top')
extract_itp('vacuum.top')
write_top('vacuum.top')
gmx('editconf',
structure='vacuum-alone',
gro='vacuum',
c=True,d='%.2f'%settings.water_buffer,
log='editconf-vacuum-room')
minimize('vacuum',method='steep')
solvate_protein(
structure='vacuum-minimized',
top='vacuum.top')
minimize('solvate')
counterions(
structure='solvate-minimized',
top='solvate',
ff_includes='ions')
minimize('counterions')
write_structure_pdb(
pdb='start-structure.pdb',
structure='counterions')
write_top('system.top')
equilibrate()
finished(state)
