Hi,
I have a simple query. i want to model my proteins as per a particular template. th pdb id is available for the same . therfore i used restraint3. i typed the following command on the terminal
./runI-TASSER.pl -pkgdir /home/nandinee/I-TASSER5.0 -libdir /home/nandinee/I-TASSER5.0/ITLIB -LBS false -EC false -GO false -seqname example2 -datadir /home/nandinee/I-TASSER5.0/data/gal3sanew -java_home /usr/bin/java -light true -hours 6 -restraint3 3V2U:C -outdir /home/nandinee/I-TASSER5.0/saexpout
and made the following change in the runI-TASSER.pl file
$restraint3 = "3V2U:A";
The job is running with the following output on the terminal:
Your setting for running I-TASSER is:
-pkgdir = /home/nandinee/I-TASSER5.0
-libdir = /home/nandinee/I-TASSER5.0/ITLIB
-java_home = /usr/bin/java
-seqname = example2
-datadir = /home/nandinee/I-TASSER5.0/data/gal3sanew
-outdir = /home/nandinee/I-TASSER5.0/saexpout
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 6
-LBS = false
-EC = false
-GO = false
Error: /usr/bin/java/bin/java does not exist.
Use /usr/bin/java instead.
1. make seq.txt and rmsinp
Your protein contains 522 residues:
> example2
MNTNVPIFSSPVRDLPRSFEQKHLAVVDAFFQTYHVKPDFIARSPGRVNLIGEHIDYCDF
SVLPLAIDVDMLCAVKILDEKNPSITLTNADPKFAQRKFDLPLDGSYMAIDPSVSEWSNY
FKCGLHVAHSYLKKIAPERFNNTPLVGAQIFCQSDIPTGGGLSSSAAFTCAAALATIRAN
MGKNFDISKKDLTRITAVAEHYVGVNNGGMDQATSVYGEEDHALYVEFRPKLKATPFKFP
QLKNHEISFVIANTLVKSNKFETAPTNYNLRVIEVTVAANALATRYSVALPSHKDNSNSE
RGNLRDFMDAYYARYENQAQPWNGDIGTGIERLLKMLQLVEESFSRKKSGFTVHEASTAL
NCSREEFTRDYLTTFPVRFQVLKLYQRAKHVYSESLRVLKALKMMTSATFHTDEDFFTDF
GRLMNESQASCDKLYECSCIETNQICSIALANGSFGSRLTGAGWGGCTIHLVPSGANGNV
EQVRKALIEKFYNVRYPDLTDEELKDAIIVSKPALGTCLYEQ
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
submit threading jobs first and run pair during threading
the setting parameters is not showing the restraint3 flag. i just want to know whether it is actually using the restraint3 flag or not i.e is it using the template which i have specified.
regards
nandinee