>Dear modellers,
>
>I've succesfully modelled a dimer with MODELLER 6. Now, I would like to
>put the substrates in my model and optimize the interactions, but I might
>be doing something wrong. I've initially placed the substrates (one per
>subunit) as they are located at the template, and I'm using the following
>alignment and top files:
>
>ALINGMENT: The template pdb corresponds to a dimer with two AMPPNP
>molecules (one per subunit). The target sequence has been written twice to
>align it with the two subunits of the template.
>
> >P1;ag_anp
>structureX:ag_anp:1:A:518:A
>MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPV---
>KKKNGLRVTPADQIDIIT-GALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQL
>DEELGHVGLAQPGSPKLINSLLENG----YLPVVSSIGVTDE------GQLMNV
>NADQAATALAATLGA-DLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVK
>VNAALDAARTLGR-----PVDIASWRHAEQLPALFNGMPMGTRILA------.
>/
>MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPV---
>KKKNGLRVTPADQIDIIT-GALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQL
>DEELGHVGLAQPGSPKLINSLLENG----YLPVVSSIGVTDE------GQLMNV
>NADQAATALAATLGA-DLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVK
>VNAALDAARTLGR-----PVDIASWRHAEQLPALFNGMPMGTRILA------.*
> >P1;akIII
>sequence:akIII:1::502
>MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVR---LVVLSASAGITNLLVALAEGLEPGE
>/-------SPALTDELVSH-GELMSTLLFVEILRER-DVQAQW-F----DVRKVMRT
>NDRFGRAE---PDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRG
>GSDYTAALLAEALHASRVDIWTDVPGIY--TTDPRVV-SAAKRIDEIAFA-EAAEMATF
>GAKVLHPATLLPAVRSDIPVFVGSSKD----PRAG-----GTLVCNKTENPP.
>/
>MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVR---LVVLSASAGITNLLVALAEGLEPGE
>/-------SPALTDELVSH-GELMSTLLFVEILRER-DVQAQW-F----DVRKVMRT
>NDRFGRAE---PDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRG
>GSDYTAALLAEALHASRVDIWTDVPGIY--TTDPRVV-SAAKRIDEIAFA-EAAEMATF
>GAKVLHPATLLPAVRSDIPVFVGSSKD----PRAG-----GTLVCNKTENPP.*
>
>
>TOP FILE: an initial model named ter_anp.pdb is given as the starting
>model. A subroutine is included to restrain the same changes in both subunits
>
>INCLUDE # Include the predefined TOP routines
>SET OUTPUT_CONTROL = 1 1 1 1 1
>SET ALNFILE = 'dimer_anp.ali' # alignment filename
>SET KNOWNS = 'ag_anp' # codes of the templates
>SET SEQUENCE = 'akIII' # code of the target
>SET ATOM_FILES_DIRECTORY = '.' # directories for input atom files
>
>SET MODEL = 'ter_anp.pdb' , GENERATE_METHOD = 'read_xyz'
>
>SET STARTING_MODEL= 1 # index of the first model
>SET ENDING_MODEL = 1 # index of the last model
> # (determines how many models to
> calculate)
>
>SET HETATM_IO = on
>CALL ROUTINE = 'model' # do homology modelling
>
>SUBROUTINE ROUTINE = 'special_restraints'
>
> SET RES_TYPES = 'ALL'
> SET ATOM_TYPES = 'ALL'
> SET SELECTION_STATUS = 'INITIALIZE'
> SET SELECTION_SEARCH = 'SEGMENT'
>
> SET SYMMETRY_WEIGHT = 0.5
> PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:''251:'
> PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '252:''502:'
> DEFINE_SYMMETRY ADD_SYMMETRY = on off
>
>
> RETURN
>END_SUBROUTINE
>
>
>The log file gives the following error:
>
>preppdf_203E> CHARMM atom type is out of range;
> Probably because GENERATE_TOPOLOGY was not called.
> Atom index, atom type: 0
>recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
>
>
>I would be very thankful if anyone could tell me what I am doing wrong and
>if there is a better strategy to do it.
>
>Many thanks in advance
Santiago
