def main():
# get current working dir
curr_dir = os.getcwd()
# set dict for using different water charges
charge_sets = {
"t3p": [-0.834, 0.417, 0.417],
"pm6": [-2.000, 1.000, 1.000]
}
# fix number of conformers per water to 1
n_conf = 5
# set number of separate MC runs
n_runs = 10
# obtain water charge set option from the command-line
prefix = sys.argv[1]
charge_set = charge_sets[prefix]
# set input directories
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
home_dir = os.path.abspath(
"../data/gramicidin/simulations/apolar_gram_%s" % prefix)
mcce_exec_dir = os.path.abspath("../code/mcce3.5")
water_dir = os.path.abspath("../data/gramicidin/water_placement")
# set filenames
src_run_prm = os.path.join(input_dir, "run.prm")
src_newtpl = os.path.join(input_dir, "new.tpl")
# run n different MC simulations, each on a different protein conf and coresponding water orientations
for n in range(n_runs):
run_dir = os.path.join(home_dir, "run_%02d" % n)
print("Run number %d, dir %s" % (n, run_dir))
if os.path.exists(run_dir):
rmtree(run_dir)
os.makedirs(run_dir)
os.chdir(run_dir)
# copy files to where MCCE will be run
copy2(src_run_prm, run_dir)
copy2(src_newtpl, run_dir)
# obtain correct step2out
src_step2out = os.path.join(input_dir, "%02d_final_step2_out.pdb" % n)
write_step2out = os.path.join(run_dir, "temp_%02d_step2_out.pdb" % n)
#print(src_step2out)
#print(write_step2out)
#copy2(src_step2out, write_step2out)
with open(src_step2out, "r") as f1, open(write_step2out, "w") as f2:
for l in f1.readlines():
if "EM" not in l:
new_l = l[:68] + " 0.000" + l[74:]
f2.write(new_l)
else:
f2.write(l)
# obtain corresponding water positions and generate conformers
init_waters = os.path.join(water_dir,
"%02d_init_wat_placement.pdb" % n)
start_index = get_last_prot_at_index(write_step2out)
coords = generate_conformers(init_waters, n_conf)
write_filename = os.path.join(run_dir, "water_confs")
write_watpdb_from_coords_ext(write_filename, coords, start_index,
charge_set)
water_conformers = write_filename + ".pdb"
# assemble full step2out and write ms_gold
last_prot_at = get_last_prot_at_index(write_step2out)
assemble_step2_out(water_conformers, write_step2out, "step2_out.pdb",
last_prot_at)
write_msgold("step2_out.pdb", "W", "HOH")
# set up MCCE run
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb",
DO_PREMCCE="f",
DO_ROTAMERS="f",
DO_ENERGY="t",
DO_MONTE="t",
MONTE_ADV_OPT="f",
MONTE_MS="t",
MONTE_REDUCE="0.0001",
BIG_PAIRWISE="1.0",
MONTE_RUNS="20")
m.write_runprm(run_dir + "/")
# run MCCE
m.write_submitsh("", run_name=str(n))
call("qsub submit.sh", shell=True)
time.sleep(10)
os.chdir(curr_dir)
def main():
curr_dir = os.getcwd()
charge_sets = {"t3p" : [-0.834, 0.417, 0.417], "pm6" : [-2.000, 1.000, 1.000]}
n_conf = 1
n_runs = 10
prefix = sys.argv[1]
charge_set = charge_sets[prefix]
# set input directories
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
run_dir = os.path.abspath("../data/gramicidin/simulations/apolar_gram")
mcce_exec_dir = os.path.abspath("../code/mcce3.5")
water_dir = os.path.abspath("../data/gramicidin/water_placement")
# set filenames
src_run_prm = os.path.join(input_dir, "run.prm")
src_step2out = os.path.join(input_dir, "00_step2_out.pdb")
src_newtpl = os.path.join(input_dir, "new.tpl")
src_ms_gold = os.path.join(input_dir, "new.tpl")
# copy files to where MCCE will be run
copy2(src_run_prm, run_dir)
copy2(src_step2out, run_dir + "/temp_step2_out.pdb")
copy2(src_newtpl, run_dir)
os.chdir(run_dir)
with open(src_step2out, "r") as f1, open("temp_step2_out.pdb", "w") as f2:
for l in f1.readlines():
if "EM" not in l:
new_l = l[:68] + " 0.000" + l[74:]
f2.write(new_l)
else:
f2.write(l)
init_waters = os.path.join(water_dir, "00_init_wat_placement.pdb")
start_index = get_last_prot_at_index(src_step2out)
coords = generate_conformers(init_waters, n_conf)
write_filename = os.path.join(run_dir, "water_confs")
write_watpdb_from_coords_ext(write_filename, coords, start_index, charge_set)
water_conformers = write_filename + ".pdb"
# assemble full step2out
last_prot_at = get_last_prot_at_index("temp_step2_out.pdb")
assemble_step2_out(water_conformers, "temp_step2_out.pdb", "step2_out.pdb", last_prot_at)
write_msgold("step2_out.pdb", "W", "HOH")
# set up MCCE run
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb",
DO_PREMCCE="f", DO_ROTAMERS="f", DO_ENERGY="t",
DO_MONTE="t", MONTE_ADV_OPT="f", MONTE_MS="t",
MONTE_REDUCE="0.0", BIG_PAIRWISE="-0.5")
m.write_runprm(run_dir + "/")
# run MCCE
#copy2(prefix + "energies.opp", "energies.opp")
for n in range(n_runs):
prefix = sys.argv[1] + "_%02d" % n
run_command = m.mcce_directory + "/mcce > " + run_dir + "/" + prefix + "_run.log"
print("Running MCCE ...")
print(run_command)
os.system(run_command)
# post-processing
copy2("ms.dat", prefix + "_ms.dat")
copy2("fort.38", prefix + "_fort.38")
copy2("head3.lst", prefix + "_head3.lst")
copy2("energies.opp", prefix + "_energies.opp")
os.chdir(curr_dir)
def main():
# get current working dir
curr_dir = os.getcwd()
# set dict for using different water charges
charge_sets = {"t3p" : [-0.834, 0.417, 0.417], "pm6" : [-2.000, 1.000, 1.000]}
# fix number of conformers per water to 1
n_conf = 5
# obtain water charge set option from the command-line
prefix = sys.argv[1]
charge_set = charge_sets[prefix]
# set input directories
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
run_dir = os.path.abspath("../data/gramicidin/simulations/wat_charges")
mcce_exec_dir = os.path.abspath("../code/mcce3.5")
water_dir = os.path.abspath("../data/gramicidin/water_placement")
# set filenames
src_run_prm = os.path.join(input_dir, "run.prm")
src_step2out = os.path.join(input_dir, "00_step2_out.pdb")
src_newtpl = os.path.join(input_dir, "new.tpl")
src_ms_gold = os.path.join(input_dir, "new.tpl")
# copy files to where MCCE will be run
copy2(src_run_prm, run_dir)
copy2(src_step2out, run_dir + "/temp_step2_out.pdb")
copy2(src_newtpl, run_dir)
# cd to directory where MCCE will be run
os.chdir(run_dir)
# generate water conformers
init_waters = os.path.join(water_dir, "00_init_wat_placement.pdb")
start_index = get_last_prot_at_index(src_step2out)
coords = generate_conformers(init_waters, n_conf)
write_filename = os.path.join(run_dir, "water_confs")
write_watpdb_from_coords_ext(write_filename, coords, start_index, charge_set)
water_conformers = write_filename + ".pdb"
# assemble full step2out
last_prot_at = get_last_prot_at_index("temp_step2_out.pdb")
assemble_step2_out(water_conformers, "temp_step2_out.pdb", "step2_out.pdb", last_prot_at)
# write ms_gold
write_msgold("step2_out.pdb", "W", "HOH")
# set up MCCE run
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb",
DO_PREMCCE="f", DO_ROTAMERS="f", DO_ENERGY="f",
DO_MONTE="t", MONTE_ADV_OPT="f", MONTE_MS="t",
MONTE_REDUCE="0.0", BIG_PAIRWISE="1.0", MONTE_RUNS="10")
m.write_runprm(run_dir + "/")
copy2(prefix + "_energies.opp", "energies.opp")
copy2(prefix + "_head3.lst", "head3.lst")
# run MCCE
run_command = m.mcce_directory + "/mcce > " + run_dir + "/" + prefix + "_run.log"
print("Running MCCE ...")
print(run_command)
os.system(run_command)
# post-processing
copy2("fort.38", prefix + "_fort.38")
copy2("energies.opp", prefix + "_energies.opp")
copy2("head3.lst", prefix + "_head3.lst")
copy2("step2_out.pdb", prefix + "_step2_out.pdb")
copy2("ms.dat", prefix + "_ms.dat")
# cd back to where started
os.chdir(curr_dir)
def main():
curr_dir = os.getcwd()
charge_sets = ["t3p", "pm6"]
chg = sys.argv[1]
if chg not in charge_sets:
sys.exit("Charge set %s not allowed!" % chg)
# input directories
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
run_dir = os.path.abspath("../data/gramicidin/simulations/wat_charges")
mcce_exec_dir = os.path.abspath("../code/mcce3.5")
water_dir = os.path.abspath("../data/gramicidin/water_placement")
# filenames
src_run_prm = os.path.join(input_dir, "run.prm")
src_step2out = os.path.join(input_dir, "fixed_step2_out.pdb")
src_newtpl = os.path.join(input_dir, "new.tpl")
src_ms_gold = os.path.join(input_dir, "new.tpl")
# copy files to where MCCE will be run
copy2(src_run_prm, run_dir)
copy2(src_step2out, run_dir + "/temp_step2_out.pdb")
copy2(src_step2out, run_dir + "/ms_gold")
copy2(src_newtpl, run_dir)
prefix = chg + "_"
n_conf = "%02d" % 1
water_conformers = os.path.join(
water_dir,
str(n_conf) + "_n_conf_perwater_" + chg + ".pdb")
# assemble full step2out
os.chdir(run_dir)
last_prot_at = get_last_prot_at_index("temp_step2_out.pdb")
assemble_step2_out(water_conformers, "temp_step2_out.pdb", "step2_out.pdb",
last_prot_at)
write_msgold("step2_out.pdb", "W", "HOH")
# set up MCCE run
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb",
DO_PREMCCE="f",
DO_ROTAMERS="f",
DO_ENERGY="f",
DO_MONTE="t",
MONTE_ADV_OPT="f",
MONTE_MS="t",
MONTE_REDUCE="0.0",
BIG_PAIRWISE="-0.5")
m.write_runprm(run_dir + "/")
# run MCCE
run_command = m.mcce_directory + "/mcce > " + run_dir + "/" + prefix + "run.log"
print("Running MCCE ...")
print(run_command)
copy2(prefix + "energies.opp", "energies.opp")
os.system(run_command)
# post-processing
copy2("fort.38", prefix + "fort.38")
copy2("energies.opp", prefix + "energies.opp")
copy2("head3.lst", prefix + "head3.lst")
copy2("ms.dat", prefix + "ms.dat")
copy2("step2_out.pdb", prefix + "step2_out.pdb")
os.chdir(curr_dir)