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')