recently we got several questions personaly or on the list about the same problem: Modeller crashes because the template structures are not overlapping. This happens when for instance one tries to model a dimer using two different template structures for each of the domains and without any structural overlap between them.
When the program starts, Modeller tries to superpose the two or more templates according to the alignmnet which does not work in these cases, of course, then stops with error.
Despite of the missing information about the structural orientation of the templates you can do the modeling if you include in your top file the following modified subroutine, just as you see below:
SUBROUTINE ROUTINE = 'transfer_xyz'
# SET ALIGNMENT_FORMAT = 'PIR' ## READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS ## MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE
READ_TOPOLOGY FILE = TOPLIB READ_PARAMETERS FILE = PARLIB
CALL ROUTINE = 'create_topology'
TRANSFER_XYZ CLUSTER_CUT = -1.0 BUILD_MODEL INITIALIZE_XYZ = OFF
WRITE_MODEL FILE = MODEL
Modeller will create models, but in case of insufficient implicit structural restraints (as e.g. bulkiness of the structures) the orientation of the individual, not overlapping parts of the model (as defined by the not overlapping templates) and the confomation of the interconnecting segments may be not accurate.
Users may impose some knowledge for the orientation of the domains, by orienting the structures prior to the modelling, or if they can introduce explicit restraints in between the independent structural parts (e.g. catalytic site between units: upper limit distance restraints among catalytic residues etc.)
Also, at the end of modelling , if the orientation of the templates was dubios one should not force the overall final superposition :
set FINAL_MALIGN3D = 0