def make_sander_input_file(parms):
lines = []
lines.append("amber.py generated sander input file")
lines.append("&cntrl")
if parms['shake_on']:
lines.append(" ntf = 2, ntb = $periodic, cut = $cutoff,")
else:
lines.append(" ntf = 1, ntb = $periodic, cut = $cutoff,")
lines.append(" igb = $solvent_state, gbsa = $surface_area, nrespa = 1,")
if parms['shake_on']:
lines.append(" ntc = 2, tol = 1.0d-8,")
else:
lines.append(" ntc = 1")
if parms['constraint_pdb']:
lines.append(" ntr = 1")
if 'n_step_minimization' in parms:
lines.append(" imin = 1, nmropt = 0,")
lines.append(" ntmin = 1, maxcyc = $n_step_minimization, ncyc = $n_step_steepest_descent,")
elif 'n_step_dynamics' in parms:
if parms['input_crds'].endswith('.rst'):
lines.append(" ntx = 5, irest = 1,")
else:
lines.append(" ntx = 1,")
lines.append(" ntpr = 50, ntave = 0, ntwr = 500, iwrap = 0, ioutfm = 0, "
"ntwx = $n_step_per_snapshot, ntwv = $n_step_per_snapshot, "
"ntwe = $n_step_per_snapshot, ")
lines.append(" nstlim = $n_step_dynamics, nscm = 50, dt = 0.001,")
if parms['periodic'] == 2:
lines.append(" ntp = 1,")
if 'thermometer_type' in parms:
lines.append(" ntt = $thermometer_type, ig = $random_seed, " + \
"temp0 = $temp_thermometer, tempi = $temp_initial, vlimit = 0.0, ")
if parms['thermometer_type'] == 2:
lines.append(" vrand = $steps_per_thermostat, ")
elif parms['thermometer_type'] == 3:
lines.append(" gamma_ln = $gamma_ln, ")
else:
raise "Can't parse parameters to run "
lines.append("/")
if parms['constraint_pdb']:
lines.append("Restrained atoms from %s" % parms['constraint_pdb'])
restraint_weight = 20.0
lines.append(str(restraint_weight))
lines.append("FIND")
lines.append("* * S *")
lines.append("* * B *")
lines.append("* * 3 *")
lines.append("* * E *")
lines.append("SEARCH")
mol = pdbstruct.Molecule()
mol.read_pdb(parms['constraint_pdb'])
for i, atom in enumerate(mol.atoms()):
if atom.bfactor > 0.0:
lines.append("ATOM %d %d" % (i+1, i+1))
lines.append("END")
lines.append("END")
return util.replace_dict("\n".join(lines), parms)
def make_namd_input_file(parms):
lines = []
lines.append("# initial structure and coordinates")
lines.append("structure $topology")
lines.append("coordinates $input_crds")
lines.append("")
lines.append("# output")
lines.append("outputName $output_name")
lines.append("binaryOutput no")
lines.append("")
lines.extend(force_field_template.splitlines())
if 'constraint_pdb' in parms:
if parms['constraint_pdb']:
lines.extend(_constraint_template.splitlines())
if 'n_step_dynamics' in parms:
lines.append("# initial temperature/velocities")
if 'input_vels' in parms and parms['input_vels'] <> "":
lines.append("velocities $input_vels")
elif 'temp_thermometer' in parms:
lines.append("temperature $temp_thermometer")
lines.append("seed $random_seed")
elif 'temp_init' in parms:
lines.append("temperature $temp_init")
lines.append("seed $random_seed")
else:
raise IndexError, "No initial velocity information for dynamics run"
if 'n_step_dynamics' in parms:
lines.extend(md_template.splitlines())
else:
lines.append("# minimization parameters")
lines.append("minimization on")
if 'temp_thermometer' in parms:
lines.append("# temperature coupling")
lines.append("langevin on")
lines.append("langevinHydrogen on")
if 'temp_couple' in parms:
lines.append("langevinTemp $temp_couple")
lines.append("langevinFile $couple_pdb")
lines.append("langevinCol B")
else:
lines.append("langevinTemp $temp_thermometer")
lines.append("langevinDamping 10.0")
return util.replace_dict("\n".join(lines), parms)
def make_namd_from_pdb(pdb, psf, out_pdb):
"""
Creates charmm .pdb and .psf file. Can only make NAMD
generate CHARMM topology files, not OPLS ones - that
requires XPLOR but I don't care. Still, if OPLS
topology files are provided - can still run.
"""
def is_non_water_hetatm(line):
if not line.startswith("HETATM"):
return False
if line[17:20] != 'HOH':
return True
return False
in_pdb = util.temp_fname('.pdb')
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, is_non_water_hetatm)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
txt = pdbtext.strip_hydrogens(txt)
txt = pdbtext.renumber_residues(txt)
f = open(in_pdb, 'w')
f.write(txt)
f.close()
name = psf.replace('.psf', '')
psfgen_in = name + ".psfgen.in"
psfgen_out = name + ".psfgen.out"
replace = { 'pdb': in_pdb,
'out_pdb': out_pdb,
'psf': psf,
'module_dir': module_dir,
'topology': 'parms/charmm22.topology'
}
template = _psfgen_template
soup = Soup(in_pdb)
chains = soup.chains()
water_names = ['WAT', "TIP", "TIP3", "HOH"]
waters = [chain for chain in chains
if chain.n_residue() > 0 and chain.residue(0).type in water_names]
chains = [chain for chain in chains if chain.n_residue() > 0 and chain.residue(0).type not in water_names]
if len(waters) > 0:
template = template.replace("# insert water", _water_psfgen_template)
water_pdb = name + ".waters.pdb"
water_soup = Soup()
for water in waters:
water_soup.insert_chain(water)
water_soup.write_pdb(water_pdb)
replace['water_pdb'] = water_pdb
chains_template = ""
for i, chain in enumerate(chains):
id = 'ch%d' % i
pdb = name + '.' + id + '.pdb'
chain_soup = Soup()
chain_soup.append_chain(chain)
chain_soup.write_pdb(pdb)
chain_replace = { 'chain_id': id, 'chain_pdb': pdb }
chain_template = _chain_psfgen_template
chains_template += util.replace_dict(chain_template, chain_replace)
template = template.replace("# insert protein", chains_template)
template = util.replace_dict(template, replace)
open(psfgen_in, "w").write(template)
os.system("psfgen %s > %s" % (psfgen_in, psfgen_out))
os.remove(in_pdb)
mol selection {backbone}
mol representation NewCartoon 0.40 20.00 2.50 0
mol addrep top
mol selection {all}
mol representation CPK 0.5 2 8 6
mol addrep top
mol smoothrep top 0 2
mol smoothrep top 1 2
"""
if len(sys.argv) < 2:
print "Usage: vmdtraj.py md"
sys.exit(1)
in_md = sys.argv[1]
parms = {"ext_top": "parm7", "ext_trj": "crd", "top": in_md + ".top", "trj": in_md + ".trj"}
if not has_files(parms["top"], parms["trj"]):
parms = {"ext_top": "gro", "ext_trj": "trr", "top": in_md + ".gro", "trj": in_md + ".trr"}
if not has_files(parms["top"], parms["trj"]):
parms = {"ext_top": "psf", "ext_trj": "dcd", "top": in_md + ".psf", "trj": in_md + ".dcd"}
if not has_files(parms["top"], parms["trj"]):
print "Can't recognize trajectories with basename", in_md
cmd_fname = util.temp_fname(".vmd")
script = util.replace_dict(s, parms)
open(cmd_fname, "w").write(script)
os.system(vmd + " -e " + cmd_fname)
os.remove(cmd_fname)