Hi Isabelle,
without the actual error message it is difficult to guess but I think the
routines were overcomplicated. The first part looks good, than I would add only
that part of the routine which deals with the cis proline question (from the
CALL ROUTINE line), because your model is already being built. An example is
included in the manual among the FAQ, num. 7.
best wishes,
Andras
>
> 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
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras