def test_set_protonate_amber(tmp_path):
gmx.show_log()
##########################################
# ## Create the topologie at PH 4.0 ###
##########################################
res_prot_dict = {
'GLH': {
'res_num': [9, 24, 31, 57]
},
'ASH': {
'res_num': [3, 70]
},
'HIP': {
'res_num': [28, 35]
},
'HID': {
'res_num': [175]
},
'HIE': {
'res_num': [214]
}
}
prot = gmx.GmxSys(name='1RXZ_ph4', coor_file=PDB_1RXZ)
prot.prepare_top(out_folder=os.path.join(tmp_path, 'top_1RXZ_ph4'),
ph=7.0,
res_prot_dict=res_prot_dict,
ff="amber99sb-ildn")
top_coor = pdb_manip.Coor(prot.coor_file)
assert top_coor.num == 4081
top_1RXZ = gmx.TopSys(prot.top_file)
assert top_1RXZ.charge() == -4
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)
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,
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_insert_peptide_vsite(tmp_path):
# Gromacs verions >= 2021 support cyclic peptides
gmx.show_log()
cyclic_pep = gmx.GmxSys(name='5vav', coor_file=PDB_5VAV)
top_coor = pdb_manip.Multi_Coor(cyclic_pep.coor_file)
assert top_coor.coor_list[0].num == 209
cyclic_pep.cyclic_peptide_top(
out_folder=os.path.join(tmp_path, 'cyclic/top'))
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_top = gmx.TopSys(cyclic_pep.top_file)
assert cyclic_top.prot_res_num() == 14
cyclic_top.display()
cyclic_pep.em(out_folder=os.path.join(tmp_path, 'cyclic/em/'),
nsteps=10,
create_box_flag=True)
cyclic_amber_pep = gmx.GmxSys(name='5vav_amber', coor_file=PDB_5VAV)
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_amber_pep.cyclic_peptide_top(out_folder=os.path.join(
tmp_path, 'cyclic/top'),
ff='amber99sb-ildn')
top_coor = pdb_manip.Coor(cyclic_pep.coor_file)
assert top_coor.num == 209
cyclic_amber_top = gmx.TopSys(cyclic_amber_pep.top_file)
print(cyclic_amber_top.charge())
cyclic_amber_pep.em(out_folder=os.path.join(tmp_path, 'cyclic/em/'),
nsteps=10,
create_box_flag=True)
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)
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)
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