[phenixbb] refinement error with ligand
Christian Roth
christian.roth at bbz.uni-leipzig.de
Wed Feb 17 08:58:47 PST 2010
Dear all,
I started a refinement of one of my structures using the GUI of phenix (Version
1.6). I used the options of adding hydrogens and dis a suimulated annealing. I
used the output file and corrected it manually using Coot. I incorporated a few
Ethylenglycol Monomers which might have bound. I merged everything wrote the
file out and loaded this pdb in the GUI. I got an error which might be du to
the fact that I didnt specify a CIF file for the ligand. I started ready set
from the GUI to check the pdb and used REEL to create a CIF File. I added the
CIF-File to the File list and tried to start again phenix.refine using the
hydrogen option but no sim. annealing. However I got always the following
error log:
# Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s)
#phil __OFF__
Command line arguments:
"/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "--
overwrite"
HOST = bbzws339
HOSTTYPE = i486-linux
VENDOR = intel
USER = roth
PID = 29983
-------------------------------------------------------------------------------
PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
Version: 1.6
Release tag: 289
Platform: intel-linux-2.6 linux
User: roth
-------------------------------------------------------------------------------
phenix.refine: Macromolecular Structure Refinement
Monomer Library directory:
"/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib"
Total number of atoms: 16881
Number of models: 1
Model: ""
Number of chains: 19
Chain: "A"
Number of atoms: 1575
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 94, 1575
Classifications: {'peptide': 94}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 87}
and so on for other chains
Chain: "R"
Number of atoms: 7
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 7
Unusual residues: {'EDO': 1}
Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1}
Classifications: {'undetermined': 1}
Number of atoms with unknown nonbonded energy type symbols: 16
"HETATM16821 HO2 EDO K 1 .*. H "
"HETATM16826 HO1 EDO K 1 .*. H "
"HETATM16828 HO2 EDO L 1 .*. H "
"HETATM16834 HO1 EDO L 1 .*. H "
"HETATM16836 HO2 EDO M 1 .*. H "
"HETATM16840 HO1 EDO M 1 .*. H "
"HETATM16842 HO2 EDO N 1 .*. H "
"HETATM16848 HO1 EDO N 1 .*. H "
"HETATM16850 HO2 EDO O 1 .*. H "
"HETATM16857 HO1 EDO O 1 .*. H "
... (remaining 6 not shown)
I looked in the pdb for this atoms, but I cannot find them.
When I use a cif file created directly by phenix elbow using command line and
when I did not use the update hydrogen button the refinement works. But the new
residues as well as the EDO molecules have no hydrogens in riding positions.
Do I have to remove all hydrogens and attach them again for every cycle?
One Refinement runs for more then 5 hours regardless I use sim annealing or
not. This seems to be very long for me. Maybe I want too many optimization
steps?
Could anyone explain me what goes wrong here. I am no so much experienced with
phenix and now I run out of ideas.
Thanks in advance
Christian
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