def pdb_to_top_and_crds(force_field, pdb, basename, solvent_buffer=10.0):
"""
Creates CHARMM .coor and .psf file for NAMD simulation.
"""
solv_dir = basename + '.solvate'
save_dir = os.getcwd()
pdb = os.path.abspath(pdb)
util.goto_dir(solv_dir)
# Remove all but protein heavy atoms in a single clean conformation
stripped_pdb = basename + '.clean.pdb'
pdbtext.clean_pdb(pdb, stripped_pdb)
# Make input script for psfgen
psfgen_psf = basename+'.psfgen.psf'
psfgen_pdb = basename+'.psfgen.pdb'
script = module_load_script
script += make_chain_loading_script(stripped_pdb, basename)
script += make_disulfide_script(stripped_pdb)
script += write_script
script = script % {
# load the included CHARMM2 atom topologies
'topology': os.path.join(data.data_dir, 'charmm22.topology'),
'out_pdb': psfgen_pdb,
'out_psf': psfgen_psf
}
psfgen_in = basename+".psfgen.in"
open(psfgen_in, "w").write(script)
data.binary('psfgen', psfgen_in, basename+'.psfgen')
util.check_output(psfgen_psf)
util.check_output(psfgen_pdb)
solvate_psf(psfgen_psf, psfgen_pdb, basename, solvent_buffer)
psf = basename+'.psf'
coor = basename+'.coor'
pdb = basename+'.pdb'
os.rename(pdb, coor)
convert_restart_to_pdb(basename, pdb)
shutil.copy(psf, save_dir)
shutil.copy(coor, save_dir)
shutil.copy(pdb, save_dir)
os.chdir(save_dir)
return psf, coor
def run_tleap(force_field, pdb, name, solvent_buffer=0.0, excess_charge=0):
"""
Generates AMBER topology and coordinate files from PDB.
Depending on whether excess_charge is non-zero, will also generate
counterions. If solvent_buffer is non-zero, will generate explicit
waters, otherwise, no waters generated. No waters is used for
implicit solvent simulations.
"""
util.check_output(pdb)
# Remove all but protein heavy atoms in a single clean conformation
tleap_pdb = name + '.clean.pdb'
pdbtext.clean_pdb(pdb, tleap_pdb)
# The restart files to be generated
top = name + '.top'
crd = name + '.crd'
# Dictionary to substitute into tleap scripts
params = {
'top': top,
'crd': crd,
'pdb': tleap_pdb,
'data_dir': data.data_dir,
'solvent_buffer': solvent_buffer,
}
# use best force-field for the 2 versions of AMBER author has tested
if 'AMBER11' in force_field:
params['amber_ff'] = "leaprc.ff99SB"
elif 'AMBER8' in force_field:
params['amber_ff'] = "leaprc.ff96"
else:
raise Exception("Don't know which version of AMBER(8|11) to use.")
# make the tleap input script
script = force_field_script
# check for a few non-standard residue that have been included
residues = [r.type for r in pdbatoms.Soup(tleap_pdb).residues()]
if 'PHD' in residues:
leaprc = open("%s/phd.leaprc" % data.data_dir).read()
script += leaprc
if 'ZNB' in residues:
leaprc = open("%s/znb.leaprc" % data.data_dir).read()
script += leaprc
script += "pdb = loadpdb %(pdb)s\n"
script += disulfide_script_and_rename_cysteines(tleap_pdb, tleap_pdb)
if 'GBSA' not in force_field:
# Add explicit waters as not GBSA implicit solvent
if excess_charge != 0:
# Add script to add counterions, must specify + or -
if excess_charge > 0:
script += "addions pdb Cl- 0\n"
else:
script += "addions pdb Na+ 0\n"
solvent_buffer = 10
params['solvent_buffer'] = solvent_buffer
script += explicit_water_box_script
script += save_and_quit_script
script = script % params
# Now write script to input file
tleap_in = name + ".tleap.in"
open(tleap_in, "w").write(script)
# Now run tleap with tleap_in
data.binary('tleap', "-f " + tleap_in, name + '.tleap')
# Check output is okay
if os.path.isfile('leap.log'):
os.rename('leap.log', name + '.tleap.log')
util.check_output(name + '.tleap.log', ['FATAL'])
util.check_output(top)
util.check_output(crd)
return top, crd
def pdb_to_top_and_crds(force_field, pdb, basename, solvent_buffer=10):
"""
Converts a PDB file into GROMACS topology and coordinate files,
and fully converted PDB file. These constitute the restart files
of a GROMACS simulation.
"""
util.check_files(pdb)
full_pdb = os.path.abspath(pdb)
save_dir = os.getcwd()
# All intermediate files placed into a subdirectory
util.goto_dir(basename + '.solvate')
# Remove all but protein heavy atoms in a single clean conformation
pdb = basename + '.clean.pdb'
pdbtext.clean_pdb(full_pdb, pdb)
# Generate protein topology in pdb2gmx_gro using pdb2gmx
pdb2gmx_gro = basename + '.pdb2gmx.gro'
top = basename + '.top'
itp = basename + '_posre.itp'
# Choose force field based on GROMACS version
if 'GROMACS4.5' in force_field:
ff = 'amber99'
elif 'GROMACS4.0' in force_field:
ff = 'G43a1'
else:
raise ValueError, "Couldn't work out pdb2gmx for " + force_field
args = '-ignh -ff %s -water spc -missing -f %s -o %s -p %s -i %s -chainsep id_or_ter -merge all' \
% (ff, pdb, pdb2gmx_gro, top, itp)
data.binary('pdb2gmx', args, basename + '.pdb2gmx')
util.check_files(pdb2gmx_gro)
# Now add a box with editconf
box_gro = basename + '.box.gro'
solvent_buffer_in_nm = solvent_buffer / 10.0
data.binary(
'editconf',
'-f %s -o %s -c -d %f -bt cubic' \
% (pdb2gmx_gro, box_gro, solvent_buffer_in_nm),
basename+'.box')
util.check_files(box_gro)
# Given box dimensions, can now populate with explict waters
solvated_gro = basename + '.solvated.gro'
data.binary(
'genbox',
'-cp %s -cs spc216.gro -o %s -p %s' \
% (box_gro, solvated_gro, top),
'%s.solvated' % basename)
util.check_files(solvated_gro)
# Neutralize with counterions using genion to place ions
# based on energy parameters processed by grompp
gro = basename + '.gro'
neutralize_system_with_salt(top, solvated_gro, basename, force_field)
util.check_files(gro)
# Make a reference PDB file from restart files for viewing and restraints
convert_restart_to_pdb(basename, basename + '.pdb')
# Copy finished restart files back into original directory
fnames = util.re_glob(
'*',
os.path.basename(basename) + r'[^\.]*\.(pdb|itp|gro|mdp|top)$')
for fname in fnames:
shutil.copy(fname, save_dir)
# Cleanup
delete_backup_files(basename)
os.chdir(save_dir)
return top, gro
def run_tleap(
force_field, pdb, name, solvent_buffer=0.0, excess_charge=0):
"""
Generates AMBER topology and coordinate files from PDB.
Depending on whether excess_charge is non-zero, will also generate
counterions. If solvent_buffer is non-zero, will generate explicit
waters, otherwise, no waters generated. No waters is used for
implicit solvent simulations.
"""
util.check_output(pdb)
# Remove all but protein heavy atoms in a single clean conformation
tleap_pdb = name + '.clean.pdb'
pdbtext.clean_pdb(pdb, tleap_pdb)
# The restart files to be generated
top = name + '.top'
crd = name + '.crd'
# Dictionary to substitute into tleap scripts
params = {
'top': top,
'crd': crd,
'pdb': tleap_pdb,
'data_dir':data.data_dir,
'solvent_buffer': solvent_buffer,
}
# use best force-field for the 2 versions of AMBER author has tested
if 'AMBER11' in force_field:
params['amber_ff'] = "leaprc.ff99SB"
elif 'AMBER14' in force_field:
params['amber_ff'] = "leaprc.ff14SB"
elif 'AMBER8' in force_field:
params['amber_ff'] = "leaprc.ff96"
else:
raise Exception("Don't know which version of AMBER(8|11|14) to use.")
# make the tleap input script
script = force_field_script
# check for a few non-standard residue that have been included
residues = [r.type for r in pdbatoms.Soup(tleap_pdb).residues()]
if 'PHD' in residues:
leaprc = open("%s/phd.leaprc" % data.data_dir).read()
script += leaprc
if 'ZNB' in residues:
leaprc = open("%s/znb.leaprc" % data.data_dir).read()
script += leaprc
script += "pdb = loadpdb %(pdb)s\n"
script += disulfide_script_and_rename_cysteines(tleap_pdb, tleap_pdb)
if 'GBSA' not in force_field:
# Add explicit waters as not GBSA implicit solvent
if excess_charge != 0:
# Add script to add counterions, must specify + or -
if excess_charge > 0:
script += "addions pdb Cl- 0\n"
else:
script += "addions pdb Na+ 0\n"
solvent_buffer = 10
params['solvent_buffer'] = solvent_buffer
script += explicit_water_box_script
script += save_and_quit_script
script = script % params
# Now write script to input file
tleap_in = name + ".tleap.in"
open(tleap_in, "w").write(script)
# Now run tleap with tleap_in
data.binary('tleap', "-f "+tleap_in, name+'.tleap')
# Check output is okay
if os.path.isfile('leap.log'):
os.rename('leap.log', name + '.tleap.log')
util.check_output(name+'.tleap.log', ['FATAL'])
util.check_output(top)
util.check_output(crd)
return top, crd
def pdb_to_top_and_crds(force_field, pdb, basename, solvent_buffer=10):
"""
Converts a PDB file into GROMACS topology and coordinate files,
and fully converted PDB file. These constitute the restart files
of a GROMACS simulation.
"""
util.check_files(pdb)
full_pdb = os.path.abspath(pdb)
save_dir = os.getcwd()
# All intermediate files placed into a subdirectory
util.goto_dir(basename + '.solvate')
# Remove all but protein heavy atoms in a single clean conformation
pdb = basename + '.clean.pdb'
pdbtext.clean_pdb(full_pdb, pdb)
# Generate protein topology in pdb2gmx_gro using pdb2gmx
pdb2gmx_gro = basename + '.pdb2gmx.gro'
top = basename + '.top'
itp = basename + '_posre.itp'
# Choose force field based on GROMACS version
if 'GROMACS4.5' in force_field:
ff = 'amber99'
elif 'GROMACS4.0' in force_field:
ff = 'G43a1'
else:
raise ValueError, "Couldn't work out pdb2gmx for " + force_field
args = '-ignh -ff %s -water spc -missing -f %s -o %s -p %s -i %s -chainsep id_or_ter -merge all' \
% (ff, pdb, pdb2gmx_gro, top, itp)
data.binary('pdb2gmx', args, basename+'.pdb2gmx')
util.check_files(pdb2gmx_gro)
# Now add a box with editconf
box_gro = basename + '.box.gro'
solvent_buffer_in_nm = solvent_buffer/10.0
data.binary(
'editconf',
'-f %s -o %s -c -d %f -bt cubic' \
% (pdb2gmx_gro, box_gro, solvent_buffer_in_nm),
basename+'.box')
util.check_files(box_gro)
# Given box dimensions, can now populate with explict waters
solvated_gro = basename + '.solvated.gro'
data.binary(
'genbox',
'-cp %s -cs spc216.gro -o %s -p %s' \
% (box_gro, solvated_gro, top),
'%s.solvated' % basename)
util.check_files(solvated_gro)
# Neutralize with counterions using genion to place ions
# based on energy parameters processed by grompp
gro = basename + '.gro'
neutralize_system_with_salt(top, solvated_gro, basename, force_field)
util.check_files(gro)
# Make a reference PDB file from restart files for viewing and restraints
convert_restart_to_pdb(basename, basename+'.pdb')
# Copy finished restart files back into original directory
fnames = util.re_glob(
'*', os.path.basename(basename) + r'[^\.]*\.(pdb|itp|gro|mdp|top)$')
for fname in fnames:
shutil.copy(fname, save_dir)
# Cleanup
delete_backup_files(basename)
os.chdir(save_dir)
return top, gro
