[phenixbb] problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:

[Pavel Afonine]

Hi Gino,

- try phenix.ready_set;
- or make a separate file with a ligand in question (make sure it has 
reasonable geometry) and run either phenix.elbow or phenix.ready_set on it.

If that doesn't help please send us the PDB file (off-list).

Pavel

On 7/18/12 9:35 PM, Gino Cingolani wrote:
> 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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