Working parameter
elbow {
input {
chemical_file_name = None
chemical_file_name_type = *auto pickle
chemical_string = """CSCCC(=N)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC=O"""
chemical_string_type = *smiles sequence
geometry_file_name = None
geometry_file_name_usage = *topology initial orientation final assist
template_file_name = None
chemical_components_code = None
residue = None
read_only = False
do_all = False
optimisation_choice = None auto *am1 mogul amber ampac gamess gaussian \
jaguar mopac nwchem orca qchem
}
defaults {
id = """NRQ"""
name = None
pH = low *neutral high
random_seed = None
add_hydrogens = None
write_hydrogens = True
write_redundant_dihedrals = False
multiple_planes = False
auto_bond_cutoff = 1.95
pdb_attributes {
resseq = 1
icode = None
chain_id = A
}
}
optimisation {
steps = None
tolerence = loose *default tight
memory = 1000Mb
energy_validation = None
third_party_apps {
nprocs = 1
method = *uhf mp2 b3lyp
basis = *am1 sto-3g 3-21g 6-31g 6-31g(d) 6-31g(d,p)
aux_basis = None
}
}
view {
view_results = *None reel molden pymol
}
output {
no_output = False
output = None
output_dir = /home/fw2080/zp/mScarlet_S1_3
pass_through_input_restraints = None
pass_through_library_restraints = None
output_file_formats = *pdb *cif pdb_ligand tripos sdf data_sheet png xyz \
maestro
data_header_file = ""
job_title = """TRUe"""
overwrite = False
console_output = *default quiet silent
chiral = *retain both enumerate
pucker = *random enumerate define
pucker_definition = ""
cis_trans = *retain enumerate
png = False
}
special {
regno = None
secondary_smiles = None
amgen_id = None
}
non_user_parameters {
opt_type = am1
input_type = smiles
use_template = False
}
}
------------------------------------------------------------------------------
electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.21.2-5419 None
- Nigel W. Moriarty ([email protected])
------------------------------------------------------------------------------
Option opt_type not available
Option input_type not available
Option job_title not available
Option use_template not available
Random number seed: 3628800
Initial processing time : 0.00 seconds
0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P
------------------------------------------------------------------------------
0123456789012345678901234567890123456789
1 2 3
CSCCC(=N)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC=O
12345 6 7 89 11 111 1 11 1 1 2 22 2
01 234 5 67 8 9 0 12 3
------------------------------------------------------------------------------
Input format is SMILES
MoleculeClass : C:16 N: 3 O: 3 S: 1 (SMILES format)
23 atoms
24 bonds
0 angles
0 dihedrals
0 rings
0 chirals
Predicted memory usage by semi-empirical method : 41Mb
Timing estimates
Python portion / ATP : 66%
c++ optimisation cycle / ATP : 51%
0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise B
0:00 Anglise Anglise Anglise Anglise Anglise Anglise Anglise Anglise Anglise A
0:00 Dihedralise Dihedralise Dihedralise Dihedralise Dihedralise Dihedralise D
0:00 Chargise Chargise Chargise Chargise Chargise Chargise Chargise Chargise C
0:00 Peptidise Peptidise Peptidise Peptidise Peptidise Peptidise Peptidise Pep
0:00 Acidise Acidise Acidise Acidise Acidise Acidise Acidise Acidise Acidise A
0:00 Ringise Ringise Ringise Ringise Ringise Ringise Ringise Ringise Ringise R
0:00 Chiralise Chiralise Chiralise Chiralise Chiralise Chiralise Chiralise Chi
0:00 Equilibriumise Equilibriumise Equilibriumise Equilibriumise Equilibriumis
0:00 ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise Z
0:00 FlattenRings FlattenRings FlattenRings FlattenRings FlattenRings FlattenR
0:00 OptimiseProgression OptimiseProgression OptimiseProgression OptimiseProgr
0:00 CheckChiralisation CheckChiralisation CheckChiralisation CheckChiralisati
0:00 FreezeDihedrals FreezeDihedrals FreezeDihedrals FreezeDihedrals FreezeDih
0:00 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H
0:00 Anglise Anglise Anglise Anglise Anglise Anglise Anglise Anglise Anglise A
0:00 Dihedralise Dihedralise Dihedralise Dihedralise Dihedralise Dihedralise D
0:00 Equilibriumise Equilibriumise Equilibriumise Equilibriumise Equilibriumis
0:00 pHise pHise pHise pHise pHise pHise pHise pHise pHise pHise pHise pHise p
0:00 ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise ZMatrise Z
0:01 Chiralise Chiralise Chiralise Chiralise Chiralise Chiralise Chiralise Chi
0:01 OptimiseProgression OptimiseProgression OptimiseProgression OptimiseProgr
0:01 Peptidise Peptidise Peptidise Peptidise Peptidise Peptidise Peptidise Pep
0:01 Peptidise Aminise Peptidise Aminise Peptidise Aminise Peptidise Aminise P
0:02 ExplodeAndOptimise ExplodeAndOptimise ExplodeAndOptimise ExplodeAndOptimi
0:05 CheckXYZRational CheckXYZRational CheckXYZRational CheckXYZRational Check
0:05 CheckZMatrixRational CheckZMatrixRational CheckZMatrixRational CheckZMatr
0:05 CheckBondRational CheckBondRational CheckBondRational CheckBondRational C
0:05 CheckAngleRational CheckAngleRational CheckAngleRational CheckAngleRation
0:05 CheckChiralRational CheckChiralRational CheckChiralRational CheckChiralRa
0:05 OptimiseHydrogens OptimiseHydrogens OptimiseHydrogens OptimiseHydrogens O
0:08 FlattenRings FlattenRings FlattenRings FlattenRings FlattenRings FlattenR
0:11 CheckChiralisation CheckChiralisation CheckChiralisation CheckChiralisati
0:11 GetSubRotationUnits GetSubRotationUnits GetSubRotationUnits GetSubRotatio
0:11 RotateSubUnits RotateSubUnits RotateSubUnits RotateSubUnits RotateSubUnit
0:11 MinimumRotation MinimumRotation MinimumRotation MinimumRotation MinimumRo
0:11 ReCentre molecule for optimisation ReCentre molecule for optimisation ReC
0:11 CheckXYZRational CheckXYZRational CheckXYZRational CheckXYZRational Check
0:11 CheckBondRational CheckBondRational CheckBondRational CheckBondRational C
0:11 ** Optimisation Manager ** Optimisation Manager ** Optimisation Manager *
Quantum method : Recife Model 1 (RM1)
Optimisation method : GDIIS
Memory (Mb) : 1000Mb
Opt steps : 60
Opt macro steps : 3
0:11 GDIISClass GDIISClass GDIISClass GDIISClass GDIISClass GDIISClass GDIISCl
GDIISClass
MoleculeClass : C:16 N: 3 O: 3 S: 1 (SMILES format)
40 atoms
41 bonds
67 angles
89 dihedrals
2 rings (groups, rings, atoms) 2 11
0 chirals
--------------------
Time Energy delta E RMS Max Step size
0:00 1 33.6832
------------------------------------------------------------------------------
Fock matrix size : 109 Closed shells : 60
Virtual Memory : 278 Mb Open shells : 0
Percentage of max : 0.00%
------------------------------------------------------------------------------
0:01 2 -7.9822 -41.6575 0.0295 0.1362 1.0765 0:00
0:02 3 -9.6995 -1.7132 0.0286 0.1316 0.6560 0:00
0:02 4 -13.3568 -3.6534 0.0277 0.1264 0.7267 0:00
0:03 5 -35.8137 -22.4530 0.0303 0.1352 0.8203 0:00
0:04 6 -44.6109 -8.7955 0.0202* 0.0793* 0.7952 0:00
0:05 7 -44.4917 0.1195 0.0202* 0.0792* 0.7859 0:02
0:07 8 -53.7576 -9.2658 0.0150* 0.0564* 0.4393 0:00
