def test_protonate_ph4_7_amber(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'),
ph=4.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4108
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == 23
##########################################
# ## Create the topologie at PH 7.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph7', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph7'),
ph=7.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
##########################################
# ## Create the topologie at PH 10.0 ###
##########################################
# Remark: Amber allow lysine unprotonated
prot = gmx.GmxSys(name='1RXZ_ph10', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph10'),
ph=10.0,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4071
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -14
def test_protonate_ph4_7_12_charmm(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'), ph=4.0)
top_coor = pdb_manip.Coor(prot.coor_file)
top_1RXZ = gmx.TopSys(prot.top_file)
if (version.parse(pdb2pqr.__version__) < version.parse("3.5")):
assert top_coor.num == 4107
assert top_1RXZ.charge() == 22
else:
assert top_coor.num == 4106
assert top_1RXZ.charge() == 21
##########################################
# ## Create the topologie at PH 7.0 ###
##########################################
prot = gmx.GmxSys(name='1RXZ_ph7', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph7'), ph=7.0)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
##########################################
# ## Create the topologie at PH 10.0 ###
##########################################
# Remark: Charmm doesn't allow lysine unprotonated
prot = gmx.GmxSys(name='1RXZ_ph10', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph10'),
ph=10.0)
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4073
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -12
type=str,
required=True)
parser.add_argument('-vsite',
action="store_true",
dest="vsite_flag",
help='Use virtual site for hydrogens')
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
if args.vsite_flag:
vsite = "hydrogens"
else:
vsite = "none"
sys_name = args.f.split("/")[-1][:-4]
md_sys = gmx.GmxSys(name=sys_name, coor_file=args.f)
md_sys.prepare_top(out_folder=args.o, vsite=vsite)
md_sys.create_box(dist=1.0, box_type="dodecahedron", check_file_out=True)
print(
"\n\nTopologie creation was sucessfull \n\tTopologie directorie :\t" +
args.o)
md_sys.display()
'default=0',
type=float,
default=0)
parser.add_argument('-gpu_id',
action="store",
dest="gpuid",
help='List of GPU device id-s to use, default=\"\" ',
default="None")
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
dt = args.dt
nsteps = 1000 * args.time / dt
sys_prod = gmx.GmxSys()
sys_prod.nt = args.nt
sys_prod.ntmpi = args.ntmpi
if args.gpuid != "None":
sys_prod.gpu_id = args.gpuid
sys_prod.extend_equi_prod(args.tpr, nsteps=nsteps)
print("\n\nProduction extension was sucessfull ")
sys_prod.display()
type=float,
default=0)
parser.add_argument('-gpu_id',
action="store",
dest="gpuid",
help='List of GPU device id-s to use, default=\"\" ',
default="None")
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
sys_min = gmx.GmxSys(name=args.name, coor_file=args.f, top_file=args.p)
sys_min.nt = args.nt
sys_min.ntmpi = args.ntmpi
if args.gpuid != "None":
sys_min.gpu_id = args.gpuid
sys_min.em_2_steps(out_folder=args.o,
name=args.name,
no_constr_nsteps=args.min_steps,
constr_nsteps=args.min_steps,
posres="",
create_box_flag=args.box)
sys_min.convert_trj(traj=False)
print("\n\nMinimisation was sucessfull \n\tMinimzed directory :\t" +
args.o)
help='Number of molecule to insert',
type=int, default=20)
parser.add_argument('-o', action="store", dest="o",
help='Output Directory')
parser.add_argument('-n', action="store", dest="name",
help='Output file name')
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
sys_raw = gmx.GmxSys(name=args.name, coor_file=args.f_sys,
top_file=args.p_sys)
mol_gmx = gmx.GmxSys(name="mol", coor_file=args.f_mol,
top_file=args.p_mol)
sys_raw.display()
mol_gmx.display()
sys_raw.insert_mol_sys(mol_gromacs=mol_gmx, mol_num=args.num_mol,
new_name=args.name, out_folder=args.o,
check_file_out=True)
print("\n\nInsertion was sucessfull \n\tSystem directory :\t"
+ args.o + "\n\tsystem coor file:\t" + sys_raw.coor_file
+ "\n\tsystem top file:\t" + sys_raw.top_file)
parser.add_argument('-o', action="store", dest="o",
help='Output Directory', type=str, required=True)
parser.add_argument('-m_steps', action="store", dest="min_steps",
help='Minimisation nsteps, default=1000', type=int,
default=1000)
parser.add_argument('-time', action="store", dest="time",
help='Vacuum equilibration time(ns), default = 1ns',
type=float, default=1)
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
dt = 0.001
step = 1000 * args.time / dt
sequence = args.seq
out_folder = args.o
em_nsteps = args.min_steps
peptide = gmx.GmxSys(name='pep_' + sequence)
peptide.create_peptide(sequence=sequence, out_folder=out_folder,
em_nsteps=em_nsteps, equi_nsteps=step)
print("\n\nPeptide Creation was sucessfull \n\tPeptide directorie :\t"
+ args.o)
peptide.display()
args = parser.parse_args()
# General args:
dt = args.dt
out_folder = args.o
sys_name = args.name
maxwarn = args.maxwarn
vsite = "hydrogens"
# Peptide args:
sequence = args.seq
em_nsteps = args.em_steps
pep_step = 1000 * args.pep_time / dt
# Create peptide:
peptide = gmx.GmxSys(name='pep_' + sequence)
peptide.nt = args.nt
peptide.ntmpi = args.ntmpi
if args.gpuid != "None":
peptide.gpu_id = args.gpuid
peptide.create_peptide(sequence=sequence,
out_folder=out_folder + "/" + sequence,
em_nsteps=em_nsteps,
equi_nsteps=pep_step,
posre_post="_pep",
vsite=vsite)
peptide.display()
# Starting system args:
coor_sys = args.f_sys
maxwarn = args.maxwarn
min_steps = args.min_steps
dt_HA = args.dt_HA
dt = args.dt
HA_step = 1000 * args.HA_time / dt_HA
CA_step = 1000 * args.CA_time / dt
CA_LOW_step = 1000 * args.CA_LOW_time / dt
prot_top_folder = args.o + "/top_prot/"
prot_min_folder = args.o + "/em_prot/"
sys_top_folder = args.o + "/top_sys/"
sys_em_equi_folder = args.o + "/em_equi_sys/"
if args.p != "None":
prot_sys = gmx.GmxSys(name=sys_name, coor_file=args.f, top_file=args.p)
else:
prot_sys = gmx.GmxSys(name=sys_name, coor_file=args.f)
prot_sys.nt = args.nt
prot_sys.ntmpi = args.ntmpi
if args.gpuid != "None":
prot_sys.gpu_id = args.gpuid
if args.p == "None":
prot_sys.prepare_top(out_folder=prot_top_folder, vsite=vsite)
prot_sys.create_box(dist=1.0, box_type="dodecahedron", check_file_out=True)
prot_sys.em_2_steps(out_folder=prot_min_folder,
name=sys_name,
no_constr_nsteps=min_steps,