# PRIMER: STEP 5
#
# This script should produce two models, 1fdx.B999901 and 1fdx.B999902.
# 
# Before you run this script, do this: ln fer2.seg.ali fer2.ali
#

INCLUDE                             # Include the predefined TOP routines

SET ALNFILE  = 'vivax.pir'           # alignment filename
SET KNOWNS   = '1drh' '3dfr' '1drf' '1dlr' '8dfr' '1dyr'
SET SEQUENCE = '1viv'               # code of the target
SET ATOM_FILES_DIRECTORY = '/lab/giulio/dhfr/vivax'    # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model 
SET ENDING_MODEL  = 10              # index of the last model
                                    # (determines how many models to calculate)
SET DEVIATION     = 4.0             # have to be >0 if more than 1 model
SET RAND_SEED     = -12312          # to have different models from another TOP file

SET WATER_IO = on
SET HETATM_IO = on
SET HYDROGEN_IO = on
SET DO_LOOPS = '1'
SET LOOP_STARTING_MODEL = 1
SET LOOP_ENDING_MODEL = 20
CALL ROUTINE = 'model'              # do homology modelling