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Is it possible to set constraints between the iron in a heme group in a protein and a ligand as a BLK ? They are not cocrystalized nor docked. I try to do it this way;
my_alignment.ali
>P1;template_protein.pdb structureX:protein : 2 : :14 : ::: : PSYQLCFIPIHH-----------h----/-*
>P1;ligand.pdb structureX:ligand: 1 : :1 : :ligand:NMR: : -----------------------h----/.*
>P1;sequence_target sequence:CYP2C9: 1 : : 13: ::: : PFYQLCFIPV-------------h----/.*
and then
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'my_alignment.ali' # alignment filename SET KNOWNS = 'my_protein' 'my_ligand' # codes of the templates SET SEQUENCE = 'my_sequence' # code of the target SET HETATM_IO = on SET STARTING_MODEL = 1 # index of the first model SET ENDING_MODEL = 5 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
SUBROUTINE ROUTINE = 'special_restraints'
ADD_RESTRAINT ATOM_IDS = 'FE : 501' 'H26 : 1' , ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 4.0 0.4 ADD_RESTRAINT ATOM_IDS = 'FE : 501' 'H25 : 1' , ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 4.0 0.2 ADD_RESTRAINT ATOM_IDS = 'FE : 501' 'H24 : 1' , ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 4.0 0.1 ADD_RESTRAINT ATOM_IDS = 'FE : 501' 'H22 : 1' , ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 4.0 0.1 ADD_RESTRAINT ATOM_IDS = 'FE : 501' 'H23 : 1' , ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 4.0 0.05 RETURN END_SUBROUTINE
I would very much appreciate some help !
Best Regards
Lovisa
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