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')
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')
sim_dir = "equilibrate"
pdb_code = '1cph'
ff = 'GROMACS4.5'
pdb_code = '2evq'
ff = 'AMBER11-GBSA'
ff = 'GROMACS4.5'
i_residue = 2
util.goto_dir(sim_dir)
# 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')
