def main():
curr_dir = os.getcwd()
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
m = MCCEParams(os.path.abspath("../code/mcce3.5"))
m.edit_parameters(DO_PREMCCE="t", DO_ROTAMERS="f", TERMINALS="t")
os.chdir(input_dir)
terminal_atoms = ['CY', 'OY', 'NT', 'C1', 'C2', 'OG']
with open('noh_test_01.pdb', "r") as oldfile, open('input_struct_01.pdb', 'w') as newfile:
for line in oldfile:
atm_name = line[13:15]
if not any(at == atm_name for at in terminal_atoms):
newfile.write(line)
m.edit_parameters(INPDB=input_dir + "/input_struct_01.pdb")
m.write_runprm(input_dir + "/")
run_command = m.mcce_directory + "/mcce > prep_struct_run.log"
os.system(run_command)
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
# 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()
init_struct_dir = os.path.abspath("../data/gramicidin/init_structures")
input_dir = os.path.abspath("../data/gramicidin/prep_structures")
mcce_dir = os.path.abspath("../code/mcce3.5")
ipece_dir = os.path.abspath("../code/ipece")
os.chdir(input_dir)
init_structs = sorted([
f for f in os.listdir(init_struct_dir)
if not f.startswith("noh") and f.endswith("pdb")
])
print(init_structs)
for index, st in enumerate(init_structs):
formatted_index = "%02d" % index
print("Processing structure: ", formatted_index)
st_infile = os.path.join(init_struct_dir, st)
st_writefile = os.path.join(init_struct_dir, "noh_" + st)
# remove hydrogens
reduce_command = "reduce -T %s > %s" % (st_infile, st_writefile)
os.system(reduce_command)
# replace termini
terminal_rep = {
'CY VAL': "CA FOR",
'OY VAL': "O FOR",
'NT TRP': "N ENA",
'C1 TRP': "CA ENA",
'C2 TRP': "CB ENA",
'OG TRP': "OG1 ENA"
}
input_struct_file = "%s_%s" % (formatted_index, "input_struct.pdb")
with open(st_writefile, "r") as oldfile, open(input_struct_file,
'w') as newfile:
for line in oldfile:
atm_res_name = line[13:20]
for terminal_atom in terminal_rep.keys():
if terminal_atom == atm_res_name:
new_name = terminal_rep[terminal_atom]
#print(line[:13] + atm_res_name + line[20:])
#print(line[:13] + new_name + line[20:])
line = line[:13] + new_name + line[20:]
#print(line)
newfile.write(line)
# generate a protein step1 file
m = MCCEParams(mcce_dir)
m.edit_parameters(INPDB=input_struct_file)
m.edit_parameters(DO_PREMCCE="t", DO_ROTAMERS="f", TERMINALS="f")
m.write_runprm(input_dir + "/")
run_command = m.mcce_directory + "/mcce > prep_struct_run.log"
os.system(run_command)
copy2("step1_out.pdb", formatted_index + "_step1_out.pdb")
# insert membrane
ipece_parm = os.path.join(ipece_dir, input_dir, "ipece.prm")
input_pdb = formatted_index + "_step1_out.pdb"
output_pdb = formatted_index + "_mem_step1_out.pdb"
# assemble ipece command and run
run_command = ipece_dir + "/ipece " + ipece_parm + " " + input_pdb + " " + output_pdb
#print(run_command)
os.system(run_command)
# run step 2
m = MCCEParams(os.path.abspath(mcce_dir))
m.edit_parameters(DO_PREMCCE="t",
DO_ROTAMERS="t",
INPDB=os.path.join(input_dir, output_pdb))
m.write_runprm(input_dir + "/")
run_command = m.mcce_directory + "/mcce > prep_struct_run.log"
os.system(run_command)
copy2("step2_out.pdb", formatted_index + "_step2_out.pdb")
# fix membrane atom names in step2
pdb = os.path.join(input_dir, formatted_index + "_step2_out.pdb")
fixed_pdb = os.path.join(input_dir,
formatted_index + "_final_step2_out.pdb")
with open(pdb, "r") as f1:
with open(fixed_pdb, "w") as f2:
lines = f1.readlines()
for l in lines:
if "EM_ _" in l:
l = l.replace("x", "C")
l = l.replace("EM_ _", "MEM M")
f2.write(l)
else:
f2.write(l)
break
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():
# 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 = 1
# set number of separate MC runs
n_runs = 1
# 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/mc_type")
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)
# get assembled full step2out
copy2("../wat_charges/" + prefix + "_step2_out.pdb", "step2_out.pdb")
copy2("../wat_charges/" + prefix + "_head3.lst", "head3.lst")
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="t",
MONTE_MS="t",
MONTE_REDUCE="0.0",
BIG_PAIRWISE="-0.5")
m.write_runprm(run_dir + "/")
# copy corresponding energy opp files into energies.opp (must ensure these runs are for 00 conf
copy2("../wat_charges/" + prefix + "_energies.opp", "energies.opp")
# run MC for n_runs
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")
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
# set number of separate MC runs
n_runs = 1
# 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/simulations/input_struct_%s/run_00" % prefix)
home_dir = os.path.abspath(
"../data/gramicidin/simulations/vdw_scaling_%s" % prefix)
mcce_exec_dir = os.path.abspath("../code/mcce3.5")
scalings = [
1.0, 0.95, 0.9, 0.85, 0.8, 0.75, 0.7, 0.65, 0.6, 0.55, 0.5, 0.45, 0.4,
0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.00
]
n_runs = len(scalings)
src_run_prm = os.path.join(input_dir, "run.prm")
src_step2out = os.path.join(input_dir, "step2_out.pdb")
src_newtpl = os.path.join(input_dir, "new.tpl")
src_head3lst = os.path.join(input_dir, "head3.lst")
src_energies = os.path.join(input_dir, "energies.opp")
src_ms_gold = os.path.join(input_dir, "ms_gold")
#scalings = scalings[:5]
n_runs = len(scalings)
# 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)
copy2(src_step2out, run_dir)
copy2(src_head3lst, run_dir)
copy2(src_energies, run_dir)
copy2(src_ms_gold, run_dir)
with open("extra.tpl", "w") as f1:
f1.write("SCALING VDW0 1.00\n")
f1.write("SCALING VDW1 1.00\n")
f1.write("SCALING VDW %s\n" % str(scalings[n]))
f1.write("SCALING TORS 1.0\n")
# set up MCCE run
extra = os.path.join(run_dir, "extra.tpl")
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb",
DO_PREMCCE="f",
DO_ROTAMERS="f",
DO_ENERGY="f",
EXTRA=extra,
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():
# get current working directory
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 = 1
# 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/vdw_scaling_new")
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)
# get assembled full step2out
copy2("../wat_charges/" + prefix + "_step2_out.pdb", "step2_out.pdb")
copy2("../wat_charges/" + prefix + "_energies.opp", "energies.opp")
copy2("../wat_charges/" + prefix + "_head3.lst", "head3.lst")
write_msgold("step2_out.pdb", "W", "HOH")
# set up MCCE run
scalings = [1.0, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50] #, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00]
n_runs = len(scalings)
for n in range(n_runs):
with open("extra.tpl", "w") as f1:
f1.write("#EXTRA energy:\n")
f1.write("# Scaling factors for non-bonded energy terms\n")
f1.write("#\n")
f1.write("# VDW0: self-vdw\n")
f1.write("SCALING VDW0 1.0\n")
f1.write("# VDW1: bkbone\n")
f1.write("SCALING VDW1 %s\n" % str(scalings[n]))
f1.write("# VDW: pairwise?\n")
f1.write("SCALING VDW %1.0\n")
f1.write("# TORS: side-chain angles\n")
f1.write("SCALING TORS 1.0\n")
#f1.write("SCALING VDW0 1.00\n")
#f1.write("SCALING VDW1 1.00\n")
#f1.write("SCALING TORS 1.0\n")
extra = os.path.join(run_dir, "extra.tpl")
m = MCCEParams(mcce_exec_dir)
m.edit_parameters(INPDB="step2_out.pdb", EXTRA=extra,
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 + "/")
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("extra.tpl", prefix + "_extra.tpl")
copy2("run.prm", prefix + "_run.prm")
copy2("ms.dat", prefix + "_ms.dat")
copy2("fort.38", prefix + "_fort.38")
copy2("head3.lst", prefix + "_head3.lst")
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():
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)