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