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