[phenixbb] Problem with LLP ligand

Folmer Fredslund folmerf at gmail.com
Wed Aug 19 02:15:54 PDT 2009


Dear Jim,

2009/8/19 James Naismith <naismith at st-andrews.ac.uk>:
> Dear All,
>                        I am trying to refine a structure which has a Lys linked to PLP. In
> the PDB this is called  LLP.
> When I take it through refine it crashes complaining about the ligand.
>
> "Sorry : Fatal problems interpreting PDB file:
>   Number of atoms with unknown nonbonded energy type symbols: 8
>   Please edit the PDB file to resolve the problems and/or supply a
>   CIF file with matching restraint definitions, along with
>   apply_cif_modification and apply_cif_link parameter definitions
>   if necessary (see phenix.refine documentation).
>   Also note that phenix.elbow is available to create restraint
>   definitions for unknown ligands.
> Traceback:
> None
> "
> I know I have to use REEL to fix this in some way. I have used REEL to
> make ligands not bound to protein before. It is how to do this when
> the ligand is covalently bound that I am stuck with.
> Any help (particularly a cif restraints file!) gratefully received.
>

I have no experience with your particular case but try and read the
part of the manual found here:
http://phenix-online.org/documentation/refinement.htm#anch78
and the following paragraphs.

But first you could try and remove the hydrogens from your LLP in the
input pdb file and see if this works (you don't mention you
resolution, so I'm guessing that you have used phenix.ready_set).

Hope this helps and that somebody else can help you more.

Best regards,
Folmer Fredslund





>
>
> best
> Jim
>
>
> -------------------------------------------------------------------------------
> Major third-party components of Phenix include:
>     Python, wxwidgets, wxPython, Boost, SCons, Clipper,
>     CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
>   Enter phenix.acknowledgments for details.
> -------------------------------------------------------------------------------
>
> Processing inputs. This may take a minute or two.
>
> Working crystal symmetry after inspecting all inputs:
>   Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90)
>   Space group: P 1 21 1 (No. 4)
>
>   Monomer Library directory:
>     "/usr/local/phenix-1.4-115/chem_data/mon_lib"
>   Total number of atoms: 13558
>   Number of models: 1
>   Model: ""
>     Number of chains: 3
>     Chain: "A"
>       Number of atoms: 6752
>       Number of conformers: 2
>       Conformer: "B"
>         Number of residues, atoms: 420, 6747
>           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
> 1, 'LLP,HE3': 1}
>           Classifications: {'peptide': 420}
>           Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
>           Chain breaks: 3
>       Conformer: "A"
>         Number of residues, atoms: 420, 6747
>           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
> 1, 'LLP,HE3': 1}
>           Classifications: {'peptide': 420}
>           Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
>           Chain breaks: 3
>           bond proxies already assigned to first conformer: 6820
>     Chain: "B"
>       Number of atoms: 6800
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 423, 6800
>           Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
> 1, 'LLP,HE3': 1}
>           Classifications: {'peptide': 423}
>           Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4}
>           Chain breaks: 3
>     Chain: "M"
>       Number of atoms: 6
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 6, 6
>           Unusual residues: {' SM': 6}
>           Classifications: {'undetermined': 6}
>           Link IDs: {None: 5}
>   Number of atoms with unknown nonbonded energy type symbols: 8
>     "ATOM   3149  HG3 LLP A 211 .*.     H  "
>     "ATOM   3151  HE3 LLP A 211 .*.     H  "
>     "ATOM   3153  HD3 LLP A 211 .*.     H  "
>     "ATOM   3155  HB3 LLP A 211 .*.     H  "
>     "ATOM   9896  HG3 LLP B 211 .*.     H  "
>     "ATOM   9898  HE3 LLP B 211 .*.     H  "
>     "ATOM   9900  HD3 LLP B 211 .*.     H  "
>     "ATOM   9902  HB3 LLP B 211 .*.     H  "
>   Time building chain proxies: 9.24, per 1000 atoms: 0.68
>
>
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-- 
Folmer Fredslund
Selma Lagerløfs Allé 21 st.
2860 Søborg
Mobil: (+45) 61 468 009
Mail: folmerf at gmail.com




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