Question regarding rigid body constrained to the Fe in a heme group

[Modeller Care <>]

non-member submission forwarded by the listowner

-------------------------------------------------------------------

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


------ End of Forwarded Message