[phenixbb] problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
Pavel Afonine
pafonine at lbl.gov
Wed Jul 18 21:42:31 PDT 2012
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)
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
More information about the phenixbb
mailing list