Hi to all:
I just made modeller work!!!!
I still don`t know what my problem was, but as I can run the examples just fine, I figured the problem were my files. Briefly, I just delete my old files and created them from scratch with nedit... My final files looked like this:
(model.top, my script):
INCLUDE # Include the predefined TOP routines SET ALNFILE = 'aln.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = '../bin/modeller6v2/examples/atom_files/' # directories SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model # (determines how many models to calculate) SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from another TOP file CALL ROUTINE = 'model' # do homology modelling
(aln.ali, my alignment file) C; First alignment >P1;1cx1 structureX:1cx1:FIRST:A:LAST:A:template:HCV: 2.50:-1.00 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSK TLAG PKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLS-------PRPVSYL KGSS GGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP AAYA AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIIC DECH STDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIF CHSK KKCDELAAKLSGLGINAVAYYRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTF TIET TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPV CQDH LEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLY RLGA VQNEVTLTHPITKYIMACMSADLEVVT*
>P1;1dnj sequence:1dnj:FIRST:@:LAST:@:model:dengue: 2.50:-1.00 GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGVYKEGTFHTMWHVTRGA VLMH KGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQVLALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFS PGTS GSPIVDRKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYL PAIV REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPV-RVPNYNLIIM DEAH FTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFPQ-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWF VPSI KAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEER VILA GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEP EREK VDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAAEGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGE RKKL KPRWLDARIYSDPLALKEFKEFAAGRK*
Hope this helps, Holton...
And thanks to all for your help!!!!
Luis