def convert_pdb_to_namd_pdb(standard_pdb, namd_pdb):
soup = Soup(standard_pdb)
for res in soup.residues():
if res.type == "ILE" and res.has_atom('CD1'):
res.atom('CD1').type = 'CD'
if res.has_atom('OXT'):
res.atom('OXT').type = 'OT2'
if res.has_atom('O'):
res.atom('O').type = 'OT1'
for atom in res.atoms():
if atom.type[0].isdigit() and atom.type[1] == "H":
atom.type = atom.type[1:] + atom.type[0]
soup.write_pdb(namd_pdb)
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)