-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ Giulio Rastelli wrote: > > Dear Roberto, > thanks for your reply. In my case, residue numbers of template and model > are the same, as I am just modeling the *same* protein with the only > difference that the template does not have a disulphide, while a disulphide > is requested in the model. I attach the .top and .log files. > Thank you very much again > > Giulio > > At 08.49 11/02/02 -0500, you wrote: > >Dear Giulio, > > > >Method 1) should work. It is difficult to know exactly what is > >happening unless you tell us more about the output you get. But a > >common mistake is to use the numbering of the template, instead of the > >numbering of the model, when specifying the RESIDUE_IDS of the residues > >to be patched. In your script, does '298' '303' correspond to the > >numbering of the cysteine residues in the template or the model? It > >should be the numbering in the model. > > > >I hope this helps. > > > >Best, > > > >Roberto > > > >-- > >Roberto Sanchez, Assistant Professor > >Structural Biology Program, Department of Physiology & Biophysics and > >Institute for Computational Biomedicine, Mount Sinai School of Medicine > >Box 1677, 1425 Madison Avenue, New York, NY 10029 > >phone +1 (212) 659 8648, fax +1 (212) 849 2456 > >http://physbio.mssm.edu/~sanchez/ > > > > > >----- Original Message ----- > >From: Giulio Rastelli giulio@caesar.unimo.it > >Date: Monday, February 11, 2002 7:48 am > >Subject: create a disulphide in a protein > > > >> 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 > >> > >> > >> > > > > > > ------------------------------------------------------------------------ > Name: align.pir > align.pir Type: Plain Text (text/plain) > Encoding: 7BIT > > Name: model.top > model.top Type: Plain Text (text/plain) > Encoding: 7BIT > > Name: model.log > model.log Type: Plain Text (text/plain) > Encoding: 7BIT > > ------------------------------------------------------------------------ > > Giulio Rastelli > Dipartimento di Scienze Farmaceutiche > Università di Modena e Reggio Emilia > Via Campi 183, 41100 Modena, ITALY > tel 0039-059-2055145 fax 0039-059-2055131