コード例 #1
0
def test_prepare_for_md(params):
    util.goto_dir(sim_dir)

    print os.getcwd()
    pdb = params['pdb']

    fetch.get_pdbs_with_http(pdb)
    full_pdb = pdb + '.pdb'
    clean_pdb = os.path.abspath(pdb) + '.clean.pdb'
    pdbtext.clean_pdb(full_pdb, clean_pdb)

    print "> Generating topologies"
    simulate.pdb_to_top_and_crds(params['ff'], clean_pdb, 'sim')

    print "> Minimizing structure"
    util.goto_dir('min')
    simulate.minimize(params['ff'], '../sim', 'min')
コード例 #2
0
ファイル: run_md.py プロジェクト: autodataming/pdbremix
def test_prepare_for_md(params):
  util.goto_dir(sim_dir)

  print os.getcwd()
  pdb = params['pdb']

  fetch.get_pdbs_with_http(pdb)
  full_pdb = pdb + '.pdb'
  clean_pdb = os.path.abspath(pdb) + '.clean.pdb'
  pdbtext.clean_pdb(full_pdb, clean_pdb)

  print "> Generating topologies"
  simulate.pdb_to_top_and_crds(params['ff'], clean_pdb, 'sim')

  print "> Minimizing structure"
  util.goto_dir('min')
  simulate.minimize(params['ff'], '../sim', 'min')
コード例 #3
0
ファイル: equilibrate.py プロジェクト: autodataming/pdbremix
# Get the PDB files from the website
fetch.get_pdbs_with_http(pdb_code)

# Format the PDB file to give one single conformation 
clean_pdb = '2evq.clean.pdb'
pdbtext.clean_pdb(pdb_code+'.pdb', clean_pdb)

# Generate restart files from PDB
simulate.pdb_to_top_and_crds(ff, clean_pdb, 'sim')

# Make a protein positional restrain_protein.pdb file
make_protein_restraint_pdb('sim', 'restrain_protein.pdb')

# minimize system (mostly water) with protein positions fixed
simulate.minimize(
    ff, 'sim', 'minwater', restraint_pdb='restrain_protein.pdb')

# heat only water to 300K, hold protein fixed
simulate.langevin_thermometer(
    ff, 'minwater', 5000, 300, 'heatwater',  50, 
    restraint_pdb='restrain_protein.pdb')

# cool water back down 10K, hold protein fixed
simulate.langevin_thermometer(
    ff, 'heatwater', 5000, 10, 'coolwater',  50, 
    restraint_pdb='restrain_protein.pdb')

# equilibrate entire system to 10K 
simulate.langevin_thermometer(
    ff, 'coolwater', 5000, 10, 'heat',  50)