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

Hi Nigel, very interesting that it does not crash for you! It crashes the same way for me on my mac book pro using the following builds: phenix-1.19.2-4158 phenix-1.21.2-5419 phenix-2.0-5716 phenix-2.0rc1-5714 as well as it crashes using the latest developers code on mac book pro and linux. Going backwards, the first build where it does not crash is phenix-1.11-2567. Are you sure you are not running something as old as this? Pavel On 9/17/25 09:05, Nigel Moriarty wrote:

Zeppelin

Thanks for the bug report. It seems to be an issue on certain OS. That is it works fine on my OSX. To move forward I suggest you substitute --opt with --mopac for a more robust solution.

Cheers

Nigel

--- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Wed, Sep 17, 2025 at 2:22 AM Martin Malý wrote:

...

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

...

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

On 16/09/2025 14:29, [email protected] wrote: 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

---

phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s