Dear Zeppelin, I don't know what is wrong here. I tried to run AceDRG from CCP4 and it worked. I will send you the output files off-list. echo "CSCCC(=N)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC=O" > molecule.smi acedrg -i molecule.smi -o acedrg_from_smiles Cheers, Martin On 16/09/2025 14:29, [email protected] wrote:
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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s