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 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 delete_backup_files(tag):
util.clean_fname(*util.re_glob('*', '^#' + tag))
def delete_backup_files(tag):
util.clean_fname(*util.re_glob('*', '^#' + tag))