[phenixbb] Phenix elbow unable to determine bonding

Ahmad Khalifa underoath006 at gmail.com
Wed May 1 13:30:57 PDT 2019


I'm not sure why I'm getting this error.  I generated restraint files for
GDP with no problems. I noticed that if I change the coordinates of my
files, I have to regenerate a new restraint files to match the new
coordinates. This time I'm getting this error that I couldn't troubleshoot:

Please find attached my gdp.pdb.


---------
['/storage/IJ/.phenix/project_data/elbow_88.eff']
---------
<function run at 0x7fbd2b4bb938>
 Working parameter
elbow {
  input {
    chemical_file_name = None
    chemical_file_name_type = *auto pickle
    chemical_string = None
    chemical_string_type = *smiles sequence
    geometry_file_name =
/storage/00_Marina_Ahmad/Tubulin/real_space_refinement/GDP.pdb
    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 ampac gamess gaussian jaguar
\
                          mopac nwchem orca qchem
  }
  defaults {
    id = """GDP"""
    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 = /storage/00_Marina_Ahmad/Tubulin/real_space_refinement/
    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 = """GDP"""
    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 = simple
    input_type = pdb_rich
    use_template = False
  }
}
 ------------------------------------------------------------------------------
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None
    - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
 ------------------------------------------------------------------------------

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

Input format is PDB

MoleculeClass :  C:10  N: 5  O:11  P: 2 (PDB format)
28 atoms
30 bonds
0 angles
0 dihedrals
0 rings
0 chirals
 Predicted memory usage by semi-empirical method : 45Mb
 Timing estimates
     Python portion         / ATP : 86%
     c++ optimisation cycle / ATP : 76%
 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
Bondise B

    Failed to determine the bonding of a fragment of the molecule.

    PDB file elbow.GDP.GDP_pdb.001.pdb written.
    Bonding file elbow.GDP.GDP_pdb.001.bonding.py written.

    Edit bonding file to reflect the desired bond.



    ALTERNATIVELY

    Re-run eLBOW with the --reel option and the molecule wil be loaded
    into REEL.  Edit the bonds and save the results as "fixed.cif" to
    allow eLBOW to load the bonding.

    You can also use a pull-down menu to push to eLBOW.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190501/7599386c/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: GDP.pdb
Type: application/octet-stream
Size: 3340 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190501/7599386c/attachment.a>


More information about the phenixbb mailing list