** MODELLER Support ** create a disulphide in a protein

[Bozidar Jerkovic <>]

Hi,

Which version of MODELLER 6 are you using? If you don't have it already,
please install MODELLER 6v1 from our web site. Also would you please send us
your input/output files (.top, .log, .pir, etc) to try to locate the
problem.

Thanks,
Bozidar


**************************************************
Dear Modellers,

Starting from a Xray structure of a protein where the 2 cysteines are
far apart, I would like to model the *same* protein with a disulphide. I
tried manual patching of disulphides in 2 ways, but none seems to work:

1) 

INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE  = '/lab/giulio/cu/homology/align.pir'
SET KNOWNS   = 'alr2'
SET SEQUENCE = 'dis'
SET ATOM_FILES_DIRECTORY = '/lab/giulio/cu/homology'
SET STARTING_MODEL= 1
SET ENDING_MODEL  = 12
SET DEVIATION     = 4.0
SET RAND_SEED     = -12312
SET HETATM_IO = on
CALL ROUTINE = 'model'
STOP
SUBROUTINE ROUTINE = 'special_patches'
 PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303'
 RETURN
END_SUBROUTINE

2)

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
SET HETATM_IO = on
READ_MODEL FILE = 'alr2'
SEQUENCE_TO_ALI ATOM_FILES = 'alr2', ALIGN_CODES= 'alr2' SEQUENCE_TO_ALI
ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'alr2.ini', ;
                ALIGN_CODES = ALIGN_CODES 'alr2-ini' GENERATE_TOPOLOGY
SEQUENCE = 'alr2-ini' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298'
'303' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ= off MAKE_RESTRAINTS
RESTRAINT_TYPE = 'stereo' ENERGY

Any suggestions? Thank you very much for your help
(PS I'm using Modeller 6)

Giulio