The new loop optimization method relies on a scoring function and optimization schedule adapted for loop modeling [Fiser et al., 2000]. The corresponding TOP routine is called when you set DO_LOOPS to 1.
The method first takes the generated model, and selects all regions around gaps in the alignment for additional loop modeling. (To select a different region for modeling, simply redefine the select_loop_atoms routine.) An initial loop conformation is then generated by simply positioning the atoms of the loop with uniform spacing on the line that connects the main-chain carbonyl oxygen and amide nitrogen atoms of the N- and C-terminal anchor regions respectively, and this model is written out to a file with the .IL extension.
Next, a number of loop models are generated from LOOP_STARTING_MODEL to LOOP_ENDING_MODEL. Each takes the initial loop conformation and randomizes it by in each of the Cartesian directions. The model is then optimized thoroughly twice, firstly considering only the loop atoms and secondly with these atoms ``feeling'' the rest of the system. The loop optimization relies on an atomistic distance-dependent statistical potential of mean force for nonbond interactions [Melo & Feytmans, 1997]. This classifies all amino acid atoms into one of 40 atom classes (as defined in $LIB/atmcls-melo.lib) and applies a potential as MODELLER cubic spline restraints (as defined in $LIB/melo-dist1.lib). Each loop model is written out with the .BL extension.
For more information, please consult the loop modeling paper [Fiser et al., 2000] or look at the loop modeling script itself, __ loop.top.
# Homology modelling by the MODELLER TOP routine 'model'. # # This can be ran with run_clustor model-loop.top, too. # # In addition to the standard overall homology modeling, at the end, this # routine also calls the thorough loop optimization routine, which generates # by default 25 loop models for each *.B9999???? model. The default # loop selection (regions around gaps) can be changed by re-defining # routine select_loop_atoms. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 0 SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files # SET STARTING_MODEL= 1 # SET ENDING_MODEL = 1 # (determines how many models to calculate) SET DO_LOOPS = 1 # do loops extensively SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 4 SET LOOP_MD_LEVEL = 'refine_1' SET MD_LEVEL = 'nothing' CALL ROUTINE = 'model' # do homology modelling