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