[phenixbb] problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
Gino Cingolani
Gino.Cingolani at jefferson.edu
Wed Jul 18 21:35:09 PDT 2012
Hi all (Nigel),
I'm trying the generate restraints for a large structure that also contains 12 ANPs, 4 ADPa and a a few more ions. When i run "phenix.elbow --do-all MR.1.pdb", phenix crashes with the following...
------------------------------------------------------------------------------
electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.8 1069
- Nigel W. Moriarty (NWMoriarty at LBL.Gov)
------------------------------------------------------------------------------
Input format is PDB
MoleculeClass : C:20 N:11 O:22 P: 5 (PDB format)
58 atoms
0 bonds
0 angles
0 dihedrals
0 rings
Molecule was trimmed
MoleculeClass : C:10 N: 6 O:12 P: 3 (PDB format)
31 atoms
0 bonds
0 angles
0 dihedrals
0 rings
Predicted memory usage by semi-empirical method : 47Mb
Timing estimates
Python portion / ATP : 100%
c++ optimisation cycle / ATP : 100%
Hydrogens may be required to determine the correct bonding
0:05 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H
Traceback (most recent call last):
File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2240, in <module>
run()
File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2038, in run
molecule = builder(molecule, options)
File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 870, in builder
pre_optimise_selections=pre_optimise_selections,
File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 1009, in ExplodeAndOptimise
opt_cycles=1,
File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 270, in OptimiseSelectedAtoms
show_geo=show_geo,
File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 673, in OptimiseCCTBXProgression
additional_restraints=additional_restraints,
File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/CCTBXMixins.py", line 262, in GetNewManager
debug=debug,
File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/geometry_manager.py", line 173, in run
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 595, in pair_proxies
check_bonded_distance_cutoff(sites_cart=sites_cart)
File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 499, in check_bonded_distance_cutoff
raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
distance: 1 - 31: 478.879
distance: 2 - 32: 603.994
distance: 5 - 33: 595.912
distance: 7 - 34: 479.110
distance: 13 - 35: 389.539
distance: 13 - 36: 559.710
distance: 14 - 37: 561.219
distance: 16 - 38: 696.942
distance: 17 - 39: 571.138
distance: 18 - 40: 497.529
distance: 19 - 41: 593.584
distance: 20 - 42: 483.447
distance: 22 - 43: 566.195
distance: 26 - 44: 561.483
distance: 26 - 45: 470.865
distance: 28 - 46: 628.947
Any clues? All nucleotides look good by eye.
Thanks,
Gino
******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab (215) 503 4595
Fax (215) 923 2117
E-mail: gino.cingolani at jefferson.edu
Website: http://www.cingolanilab.org
******************************************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge") Dante,
The Divine Comedy (Inferno, XXVI, vv. 119-120)
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