Dear colleagues,
I�m facing a problem with Modeller6, and although it seems to be a common one (I�ve seen similar requests in the list archives), I just couldn�t fix it reading the previous posts nor the FAQ.
The PDB file I�m using as a template starts at residue 8 and ends at residue 315. So, my alignement is as follows: =======================================================
C; A sample alignment in the PIR format; used in tutorial >P1;1DKU structureX:1DKU:8 : :315 : :PRPP:bacilo: 1.90: 0.19 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGY ARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLE--DIVIVSPDHGGVTRARKLADRLKAPIAIIDK RRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKK-IERFKQLSVGP LLAEAIIRVHEQQSVSYLFS----* >P1;HUMA sequence:HUMA:8 : :315 : :PRPP:Homo sapiens: 2.00:-1.00 NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPY ARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHK ERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISM ILAEAIRRTHNGESVSYLFSHVPL*
=======================================================
The .top file was directly edited from the example model-default.top, and is as follows:
====================================================== # Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'ALIN.pir' # alignment filename SET KNOWNS = '1DKU' # codes of the templates SET SEQUENCE = 'HUMA' # code of the target SET ATOM_FILES_DIRECTORY = '/mod6v2/examples/tutorial-model/' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
=====================================================
Both the alignement file "ALIN.pir" and PDB file "1DKU.pdb" are on the /mod6v2/examples/tutorial-model/ directory. But although the program actually opens this pdb file, it shows this message:
rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 309 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Does anybody has any hint on how to fix this problem?
Thanks in advance, Lucas Bleicher
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