def main():
parser = argparse.ArgumentParser(description='Perform SMD runs for dynamic undocking')
parser.add_argument('-i', '--input', help='Equilibrated system as input')
parser.add_argument('-p', '--pickle', help='Pickle file')
parser.add_argument('-n', '--num-runs', type=int, help='Number of SMD runs.')
# parser.add_argument('-o', '--output', help="PDB output")
parser.add_argument('-l', '--md-len', type=float, help='MD run length.')
parser.add_argument('-d', '--start-dist', type=float, help='Starting distance')
parser.add_argument('-v', '--init-velocity', type=float, help='Initial velocity')
parser.add_argument('--gpu-id', type=int, help='GPU ID (optional); if not specified, runs on CPU only.')
args = parser.parse_args()
shutil.copyfile(args.input, "equil.chk")
shutil.copyfile(args.pickle, "complex_system.pickle")
# Now do the MD
# remember start_dist
for i in range(args.num_runs):
if i == 0:
md_start = "equil.chk"
else:
md_start = "md_" + str(i - 1) + ".chk"
log_file = "md_" + str(i) + ".csv"
perform_md(
md_start,
"md_" + str(i) + ".chk",
log_file,
"md_" + str(i) + ".pdb",
md_len=args.md_len,
gpu_id=args.gpu_id,
)
# Open the file and check that the potential is stable and negative
if not check_if_equlibrated(log_file, 3):
print("SYSTEM NOT EQUILIBRATED")
sys.exit()
# Now find the interaction and save to a file
run_steered_md(
300,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_300.csv",
"smd_" + str(i) + "_300.dat",
"smd_" + str(i) + "_300.pdb",
"smd_" + str(i) + "_300.dcd",
args.start_dist,
init_velocity=args.init_velocity,
gpu_id=args.gpu_id,
)
run_steered_md(
325,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_325.csv",
"smd_" + str(i) + "_325.dat",
"smd_" + str(i) + "_325.pdb",
"smd_" + str(i) + "_325.dcd",
args.start_dist,
init_velocity=args.init_velocity,
gpu_id=args.gpu_id,
)
def run_simulation(
prot_file,
mol_file,
prot_code,
prot_int,
cutoff,
init_velocity,
num_smd_cycles,
gpu_id,
md_len,
params,
):
if not os.path.isfile("equil.chk"):
# A couple of file name
orig_file = prot_file
chunk_protein = "protein_out.pdb"
chunk_protein_prot = "protein_out_prot.pdb"
# Do the removal of buffer mols and alt locs
if params.get("remove_buffers", True):
prot_file = remove_prot_buffers_alt_locs(prot_file)
# Do the chunking and the protonation
if params.get("prep_chunk", True):
# Chunk
chunk_with_amber(mol_file, prot_file, prot_int, chunk_protein,
cutoff, orig_file)
# Protontate
disulfides = find_disulfides(chunk_protein)
do_tleap(chunk_protein, chunk_protein_prot, disulfides)
else:
chunk_protein_prot = prot_file
# Paramaterize the ligand
mol2_file = params.get("mol2_file_prepped", None)
if not mol2_file:
results = prep_lig(mol_file, prot_code)
mol2_file = results[0]
prepare_system(mol2_file, chunk_protein_prot)
# Now find the interaction and save to a file
results = find_interaction(prot_int, orig_file)
startdist = params.get("distance", results[2])
# Now do the equlibration
do_equlibrate(gpu_id=gpu_id)
else:
# Now find the interaction and save to a file
results = find_interaction(prot_int, prot_file)
startdist = params.get("distance", results[2])
# Open the file and check that the potential is stable and negative
if not check_if_equlibrated("density.csv", 1):
print("SYSTEM NOT EQUILIBRATED")
sys.exit()
if params.get("just_equilib", False):
print("SYSTEM FENISHED EQULIBRATING")
return
# Now do the MD
for i in range(num_smd_cycles):
if i == 0:
md_start = "equil.chk"
else:
md_start = "md_" + str(i - 1) + ".chk"
log_file = "md_" + str(i) + ".csv"
perform_md(
md_start,
"md_" + str(i) + ".chk",
log_file,
"md_" + str(i) + ".pdb",
md_len=md_len,
gpu_id=gpu_id,
)
# Open the file and check that the potential is stable and negative
if not check_if_equlibrated(log_file, 3):
print("SYSTEM NOT EQUILIBRATED")
sys.exit()
# Now find the interaction and save to a file
run_steered_md(
300,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_300.csv",
"smd_" + str(i) + "_300.dat",
"smd_" + str(i) + "_300.pdb",
"smd_" + str(i) + "_300.dcd",
startdist,
init_velocity=init_velocity,
gpu_id=gpu_id,
)
run_steered_md(
325,
"md_" + str(i) + ".chk",
"smd_" + str(i) + "_325.csv",
"smd_" + str(i) + "_325.dat",
"smd_" + str(i) + "_325.pdb",
"smd_" + str(i) + "_325.dcd",
startdist,
init_velocity=init_velocity,
gpu_id=gpu_id,
)
from duck.steps.normal_md import perform_md
from duck.steps.steered_md import run_steered_md
# Define these
prot_code = "MURD-x0374"
prot_int = "A_LYS_311_N"
# Cutoff for the sphere
# Now it does the magic
results = get_from_prot_code(prot_code)
prot_file = results[0]
# Now find the interaction and save to a file
results = find_interaction(prot_int, prot_file)
startdist = results[2]
for i in range(20):
if i == 0:
md_start = "equil.chk"
else:
md_start = "md_" + str(i - 1) + ".chk"
perform_md(md_start,
"md_" + str(i) + ".chk",
"md_" + str(i) + ".csv",
"md_" + str(i) + ".pdb",
md_len=0.5)
# Now find the interaction and save to a file
run_steered_md(300, "md_" + str(i) + ".chk", "smd_" + str(i) + "_300.csv",
"smd_" + str(i) + "_300.dat", "smd_" + str(i) + "_300.pdb",
"smd_" + str(i) + "_300.dcd", startdist)
run_steered_md(325, "md_" + str(i) + ".chk", "smd_" + str(i) + "_325.csv",
"smd_" + str(i) + "_325.dat", "smd_" + str(i) + "_325.pdb",
"smd_" + str(i) + "_325.dcd", startdist)