def pdb2gmx_periodic(pdb, watermodel, forcefield):
# Assume a pdb2gmx wrapper script for periodic molecules is in the same directory as this file.
periodic_pdb2gmx = os.path.dirname(os.path.realpath(__file__)) + '/gmx-pdb2gmx-wrapper-periodic-dna.sh'
args=' '.join(['-water', watermodel, '-ff', forcefield, '-f', pdb])
xsh(' '.join([periodic_pdb2gmx, args]))
def neutralize_box(gro='conf.gro', top='topol.top', tpr='topol.tpr'):
args = ' '.join(
['-neutral', '-pname', 'NA', '-p', 'topol.top', '-o', 'conf.gro'])
interactive_args = 'SOL'
cmd = ' '.join(['echo -e', interactive_args, '|', gmx, 'genion', args])
stdout = xsh(cmd)
def make_box_for_periodic_dna(gro='conf.gro'):
# Make a box for a DNA molecule that is periodically connected in the z-direction.
# The box angles (naming as in gmx manual).
# Here vectors a and b lie in the xy-plane, and are 60 deg apart.
# vector c is parallel to the z axis
bc, ac, ab = 90, 90, 60
# Very simple measure of the diameter along each dimension:
coords = gmxb.read_gro_coordinates(gro)
diameter = coords.max(0) - coords.min(0)
# Dna is roughly circular in x and y. Use the x diameter and add 2 nm
# to ensure that periodic images are ~ 2 nm apart.
a = diameter[0] + 2.0
b = a
# The z box length should equal the molecule length since we are making a
# periodic molecule.
c = diameter[-1]
# Make the box with editconf
angles = ' '.join([str(bc), str(ac), str(ab)])
lengths = ' '.join([str(a), str(b), str(c)])
out = 'conf.gro'
args = ' '.join(['-angles', angles, '-box', lengths, '-o', out])
stdout = xsh(' '.join([gmx, 'editconf', args]))
def solvate_box(gro='conf.gro', top='topol.top', tpr='topol.tpr'):
args = ' '.join(['-cp', gro, '-p', top, '-cs', '-o', 'conf.gro'])
stdout = xsh(' '.join([gmx, 'solvate', args]))
def example_build(make_clean=False):
# External parameters are assumed to be present
scripts_dir = os.path.dirname(os.path.realpath(__file__))
external_params_dir = scripts_dir + '/../external-parameters'
# Note: the pdb files could be generated from a sequence from within here calling some modeling tool like x3dna.
# Another option is using the pmx python library. However, the current modeling capabilities of pmx for DNA is
# limited and not optimal for generating the periodic DNA topologies since the phosphates at the end residues are
# missing in the moddel.
pdb_dir = external_params_dir + '/pdbs/vary-num-T'
pdbs = [
'/'.join([pdb_dir, f]) for f in os.listdir(pdb_dir)
if f.endswith('.pdb')
]
# Build specifications (model parameters)
build_list = [{
'name': 'charmm',
'ff': 'charmm27',
'water': 'tip3p',
'ffdir': None
}, {
'name': 'amber',
'ff': 'amber99bsc1',
'water': 'spce',
'ffdir': external_params_dir + '/forcefields/amber99bsc1.ff'
}]
def sysname(pdb):
return pdb.split('.pdb')[0].split('/')[-1]
startdir = os.getcwd()
# Here, each pdb is built with each model.
for pdb, specs in zip(
len(build_list) * pdbs,
len(pdbs) * build_list,
):
print 'Building:', sysname(pdb), specs['name']
# Define the directory hierarchy. Infer system name from pdb file.
build_dir = '/'.join([startdir, specs['name'], sysname(pdb), 'build'])
if make_clean:
xsh('rm -rf ' + build_dir)
xsh('mkdir -p ' + build_dir)
# Add external parameters if needed
if specs['ffdir']:
xsh('cp -r ' + specs['ffdir'] + ' ' + build_dir)
# Build the gmx system
os.chdir(build_dir)
build_periodic_dna(pdb,
forcefield=specs['ff'],
watermodel=specs['water'])
os.chdir(startdir)
# Add runs. Here, each run is added to each build.
run_list = [
{
'name': 'em',
'mdp': mdp_periodic_dna(specs['name'], 'em'),
'selections': []
},
{
'name': 'npt',
'mdp': mdp_periodic_dna(specs['name'], 'npt'),
'selections': []
},
]
# Add AWH runs, calculate PMF for some base pairs (bp). The reaction coordinate requires
# bp-specific atom selections. Here, generate all possible selections, then specify which
# bp is targeted in the mdp-file (could also generate only the selections needed for the
# target bp and use one mdp file).
target_basepairs = get_target_basepair_resids(build_dir + '/conf.gro')
for resid1, resid2 in target_basepairs:
name1, name2 = ['resid' + str(resid) for resid in [resid1, resid2]]
awh_sel = basepair_distance_selections(resid1,
resid2,
name1=name1,
name2=name2)
awh_mdp = gmxb.merge_mdps([
mdp_periodic_dna(specs['name'], 'npt'),
awh_basepair_dist_mdp(name1, name2), {
'nsteps': '100000000'
}
])
# Add the run specs (mdp and selections) for this base pair
run_list.append({
'name': '-'.join(['awh', name1, name2]),
'mdp': awh_mdp,
'selections': awh_sel
})
# Put the run directory on the same level as the build director
print 'Adding runs:'
for run in run_list:
print run['name']
run_dir = '/'.join(
[startdir, specs['name'],
sysname(pdb), run['name']])
if make_clean:
xsh('rm -rf ' + run_dir)
xsh('mkdir -p ' + run_dir)
template_dir = run_dir + '/template'
gmxb.make_run_template(build_dir,
run['mdp'],
template_dir,
selections=run['selections'])