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(a)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.
