def do_solvate(
name='solvate', # name of run part; used as dirname
prev_conf='../conf.gro', # input conformation
prev_ndx='../index.ndx', # input index file
gro_cgpair='', # gro files?
nat_cgpair=0 # nr of atoms?
):
# solvate structure with cg water
# create and change to run dir:
prev_dir = os.getcwd()
dir = name
ot.GotoDir(dir)
# link input conformation file:
this_conf = 'conf.gro'
ot.symlink(prev_conf, this_conf)
# solvate structure with cg water
optionlist = [
'-cp ' + this_conf,
'-cs ' + env.mffstruct.replace(' ', '\ ') + '/water.gro', '-vdwd 0.19'
]
result = gmx.g_genbox(optionlist, log='genbox.err')
if result: return result
# make a new ndx file of the solvated structure
outgro = 'out.gro'
tmpndx = 'tmp.ndx'
optionlist = ['-f ' + outgro, '-o ' + tmpndx]
stdin = ['q'] # just quit; writes out all default index groups
result = gmx.g_make_ndx(optionlist, log='make_ndx.err', stdin=stdin)
if result: return result
ngroups = st.ngroups_in_ndx(tmpndx)
os.remove(tmpndx)
ndx_sol = re.sub('.ndx', '_sol.ndx', prev_ndx)
ndxlist = gmx.gen_ndxUIlist(ngroups, gro_cgpair, nat_cgpair)
optionlist = [
'-f ' + outgro,
'-o ' + ndx_sol,
]
result = gmx.g_make_ndx(optionlist, log='make_ndx.err', stdin=ndxlist)
if result: return result
# return to original (parent) dir
os.chdir(prev_dir)
# next step needs to know our dirname and output index and gro files:
return result, dir, ndx_sol, outgro
def do_simulations(
pdbfile, # input PDB file
pair, # set of chains
distances, # list of distances
boRun=True, # start production run after equilibration
pull='cons', # type of pull: _cons_traints or _umbrella_
nsteps=None # nsteps for production run (None=default)
):
# make directory for output:
pdbase = pdbfile.split('.pdb')[0]
dir = pdbase
if (not (os.path.exists(dir) and os.path.isdir(dir))):
os.mkdir(dir)
os.chdir(dir)
# create symlink to input pdbfile
ot.symlink('../' + pdbfile, pdbfile)
# create CG (coarse-grained MARTINI) representation of protein:
cggro_merged, cgndx_merged, cg_stable_itppair, \
gro_cgpair, nat_cgpair, fgpair = \
mfft.do_fg2cg(pdbfile, pair)
print("After CG2FG got output files:", cggro_merged, cgndx_merged,
cg_stable_itppair, gro_cgpair, nat_cgpair, fgpair)
groups = []
for i in gro_cgpair:
groups.append(re.sub('_cg.gro', '', i))
root_dir = os.getcwd()
for distance in sorted(distances):
result = ps.do_pullsim(root_dir, distance, cggro_merged, cgndx_merged,
groups, cg_stable_itppair, nat_cgpair, pdbase,
fgpair, gro_cgpair, boRun, pull, nsteps)
if result:
print("pullsim failed in", os.getcwd())
# make empty file to flag this error
open("FAILED", 'w').close()
os.chdir(root_dir)
def do_one_sim(
name='em_vac', # name of run part; used as dirname
run_type='em', # type of run: em, em_posre,
# md_pull_eq, md_pull_prod, md_umbr_prod
top_type='cg', # type of topology: cg, cg_posre
prev_conf='../conf.gro', # input conformation
prev_ndx=None, # input index file
pdbase='system', # name for system/molecule in topology file
cg_stable_itppair='', # some itp file?
fgpair='', # some itp file?
posrepair=[], # position restraints itp file,
posredir=None, # dir where to find pr itp file
groups='', # index groups for chains across interface
nat_cgpair=[], # nr of atoms in each chain
sdistance=None, # con/restraint distance
boRun=True # start mdrun
):
# create and change to run dir:
prev_dir = os.getcwd()
dir = name
ot.GotoDir(dir)
# link input conformation file:
this_conf = 'conf.gro'
ot.symlink(prev_conf, this_conf)
# generate MD parameter file:
if sdistance:
# add pull groups to MDP:
bbgroups = [group + '_backbone' for group in groups]
else:
bbgroups = []
mdpfile = mdp.generate_mdp(run_type, sdistance, bbgroups)
# we rely on being two dir levels deep: e.g., 'd2.30/md_sol_pr'
for file in cg_stable_itppair:
ot.symlink('../../' + file, './' + file)
# link to Martini base topology files:
if ot.symlink(env.mffFF + '/' + env.mffitp, env.mffitp): exit(-1)
if ot.symlink(env.mffFF + '/' + env.mffions, env.mffions): exit(-1)
if prev_ndx:
# link index file
this_ndx = os.path.split(prev_ndx)[1] # returns ['/path', 'file']
ot.symlink(prev_ndx, this_ndx)
else:
this_ndx = None
ret_posrepair = []
if posrepair:
# make local links:
this_posrepair = []
for file in posrepair:
this = os.path.split(file)[1] # returns ['/path', 'file']
ot.symlink('../' + posredir + '/' + file, this)
this_posrepair.append(this)
posrepair = this_posrepair
# now trim pathname from posrepair file names:
elif this_ndx:
# generate posre files:
print("Gen POSRE", this_ndx, this_conf, groups, nat_cgpair)
posrepair = st.gen_posre(this_ndx, this_conf, groups, nat_cgpair)
print("Got POSRE", posrepair)
ret_posrepair = posrepair
topfile = top.generate_top(top_type, pdbase, cg_stable_itppair, fgpair,
this_conf, posrepair)
# grompp
optionlist = ['-f ' + mdpfile, '-c ' + this_conf, '-p ' + topfile]
if this_ndx: optionlist.append('-n ' + this_ndx)
if run_type.startswith('em'): optionlist.append('-maxwarn 1')
elif run_type.startswith('md'): optionlist.append('-maxwarn 3')
result = gmx.g_grompp(optionlist, log='grompp.err')
# return immediately if error occurred
if result: return result, dir, ret_posrepair
# mdrun
if boRun:
optionlist = ['-s topol.tpr']
result = gmx.g_mdrun(optionlist, log='md.err')
else:
print('Ready for production in', os.getcwd())
print('option list', optionlist)
# return to original (parent) dir
os.chdir(prev_dir)
# next step needs to know our dirname, and posre files
return result, dir, ret_posrepair
def do_pullsim(root_dir,
distance,
cggro_merged,
cgndx_merged,
groups,
cg_stable_itppair,
nat_cgpair,
pdbase,
fgpair,
gro_cgpair,
boRun=True,
pull='cons',
nsteps=None):
os.chdir(root_dir)
# check if distance is string or float:
try:
distance += 0.0
# is float, make string version
sdistance = str(distance)
except TypeError:
# is not float
try:
sdistance = distance + ''
distance = float(sdistance)
except TypeError:
print('Unknown type for distance:', distance, type(distance))
# make dir for this distance and cd to dir
d_dir = os.getcwd() + '/d' + sdistance
ot.GotoDir(d_dir)
ot.symlink(root_dir + '/' + cggro_merged, './' + cggro_merged)
ot.symlink(root_dir + '/' + cgndx_merged, './' + cgndx_merged)
# displace structure
dcom_of_cgpdb = ct.com_dist(cggro_merged, cgndx_merged)
cggro_disp = ct.displace_struct(dcom_of_cgpdb, groups, sdistance,
cggro_merged, cgndx_merged)
# center structure in box
cggro_cntr = re.sub('.gro', '_cntr.gro', cggro_disp)
# distance to box edge should be more than mindist+0.5*rcut (rcut = 1.2 nm)
distance_to_box_edge = 1.0 + st.mindist_between_groups(
cggro_merged, cgndx_merged, groups)
optionlist = [
'-f ' + cggro_disp,
'-o ' + cggro_cntr,
# use default rectangular/triclinic; alternate box shapes:
# '-bt cubic',
'-bt dodecahedron',
'-c',
'-princ',
'-d ' + str(distance_to_box_edge)
]
result = gmx.g_editconf(optionlist, log='editconf.err', stdin=['0'])
if result: return result
# neutralize the total structure
for itp in cg_stable_itppair:
ot.symlink(root_dir + '/' + itp, './' + itp)
cggro_neutral = st.neutralize(cggro_cntr, cg_stable_itppair, nat_cgpair)
# vacuum energy minimization
result, em_vac_dir, ignore = \
do_one_sim(name='em_vac',
run_type='em',
top_type='cg',
prev_conf='../'+cggro_neutral,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair
)
if result: return result
# vacuum energy minimization using position restraints
result, em_vac_pr_dir, posrepair = \
do_one_sim(name='em_vac_posre',
run_type='em_posre',
top_type='cg_posre',
prev_conf='../'+em_vac_dir+'/confout.gro',
prev_ndx ='../../'+cgndx_merged,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair,
groups=groups,
nat_cgpair=nat_cgpair
)
if result: return result
# solvate structure with cg water
result, solvate_dir, cgndx_sol, outgro = \
do_solvate(name='solvate',
prev_conf = '../'+em_vac_pr_dir+'/conf.gro',
prev_ndx = cgndx_merged,
gro_cgpair = gro_cgpair,
nat_cgpair = nat_cgpair
)
if result: return result
# solution energy minimization using position restraints
result, em_sol_pr_dir, ignore = \
do_one_sim(name='em_sol_posre',
run_type='em_posre',
top_type='cg_posre',
prev_conf='../'+solvate_dir+'/'+outgro,
prev_ndx ='../'+solvate_dir+'/'+cgndx_sol,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair,
posrepair=posrepair,
posredir=em_vac_pr_dir
)
if result: return result
# solution md using position restraints
result, md_sol_pr_dir, ignore = \
do_one_sim(name='md_sol_posre',
run_type='md_posre',
top_type='cg_posre',
prev_conf='../'+em_sol_pr_dir+'/confout.gro',
prev_ndx ='../'+solvate_dir+'/'+cgndx_sol,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair,
posrepair=posrepair,
posredir=em_vac_pr_dir
)
if result: return result
# solution equilibration md run
result, md_sol_eq_dir, ignore = \
do_one_sim(name='md_sol_eq',
run_type='md_pull_eq',
top_type='cg',
prev_conf='../'+md_sol_pr_dir+'/confout.gro',
prev_ndx ='../'+solvate_dir+'/'+cgndx_sol,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair,
groups=groups,
nat_cgpair=nat_cgpair,
sdistance=sdistance
)
if result: return result
# solution production md run
if pull == 'cons': run = 'md_pull_prod'
elif pull == 'umbr': run = 'md_umbr_prod'
else:
print("Unknown pull option", pull)
exit(-1)
result, md_sol_prod_dir, ignore = \
do_one_sim(name='md_sol_prod',
run_type=run,
top_type='cg',
prev_conf='../'+md_sol_eq_dir+'/confout.gro',
prev_ndx ='../'+solvate_dir+'/'+cgndx_sol,
pdbase=pdbase,
cg_stable_itppair=cg_stable_itppair,
fgpair=fgpair,
groups=groups,
nat_cgpair=nat_cgpair,
sdistance=sdistance,
boRun=boRun
)
if result: return result
os.chdir(d_dir)