>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