Hi,
we are trying to generate 3D-models for a short peptide, on the basis of
two template structures. We would like to restrain the mainchain dihedral
angles in the central region of our peptide during the modelling
procedure.
To do this, we tried to modify the following input file which allowed us
to use the 'model' routine and some special restraints at the same time.
=======================================================================
#Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 2 2 2 2 2
SET ALNFILE = 'ali1.pir' # alignment filename
SET KNOWNS = 'sero_c' 'sero_o' # codes of the templates
SET SEQUENCE = 'agen7' #code of the target
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
CALL ROUTINE = 'model' # do homology modelling
STOP
SUBROUTINE ROUTINE = 'special_restraints'
SET ADD_RESTRAINTS = on
MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '3' '6' RETURN
END_SUBROUTINE
==========================================================================
We thought it would be possible to modify the 'special_restraints' routine
on the basis of the example file enforcing a cis conformation for a
proline residue:
=========================================================================#
Example for: ADD_RESTRAINT, DELETE_RESTRAINT
# This will enforce cis conformation for Pro-56.
# Make a model and stereochemical restraints:
DEFINE_STRING VARIABLES = ATOM_IDS1 ATOM_IDS2
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ;
ALIGN_CODES = ALIGN_CODES '1fas-ini' GENERATE_TOPOLOGY
SEQUENCE = '1fas-ini'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
# Change the Pro-56 restraint from trans to cis:
CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:56' 'C:56' 'N:57' 'CA:57', ;
ATOM_IDS2 = 'CA:56' 'C:56' 'N:57' 'CA:57'
WRITE_RESTRAINTS FILE = '1fas.rsr'
ENERGY
SUBROUTINE ROUTINE = 'cispeptide'
# Delete the old restraint on the same atoms:
DELETE_RESTRAINT ATOM_IDS = ATOM_IDS1
# Add the new restraint:
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 3.141593 0.087
DELETE_RESTRAINT ATOM_IDS = ATOM_IDS2
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 0.0 0.087
RETURN
END_SUBROUTINE
=========================================================================
Doing this, we succeeded in writing the correct restraints file, but the
'model' routine stopped and no new model was generated.
We thought maybe it might be necessary to proceed in two steps:
1. writing the restraints file
2. reading this restraint file prior to run the 'model' routine.
Any help or suggestion would be appreciated.
Thank you
Isabelle