I solved the problem. This was the original top file:

INCLUDE # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file

SET ALNFILE = 'alignment1.txt' # alignment filename

SET KNOWNS = '1PTQ' # codes of the templates

SET SEQUENCE = 'pkci' # code of the target

#SET TOPOLOGY_MODEL = 1

SET HETATM_IO = on

SET TOPLIB = '$(LIB)/top.lib'

SET PARLIB = '$(LIB)/par.lib'

#SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files

SET STARTING_MODEL= 1 # index of the first model

SET ENDING_MODEL = 1 # index of the last model

# (determines how many models to calculate)

CALL ROUTINE = 'model' # do homology modelling

SUBROUTINE ROUTINE = 'special_restraints'

ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

RETURN

END_SUBROUTINE

I was using top.lib (all hydrogen topology). When I changed it to top_heav things work.

Alfredo Cardenas