[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] help with modelling protein-DNA complex



Hi,

I have looked at the manual and previous queries posted on this reoccuring subject but am unable to get modeller to model a protein-DNA complex where I treat the DNA as a rigid body.
All I get back are models of the protein with no DNA present.

I have done 3 things

1. Changed my pdb file so the DNA entry has HETATM and BLK (a sample below) :
HETATM 1043  O5* BLK C 100      31.258  -2.296  76.212  1.00 81.62      
DNA1 O HETATM 1044  C5* BLK C 100      29.867  -2.121  76.367  1.00 
69.89      DNA1 C
2. Included in my alignment file a '.' for each BLK residue and a '/' to 
signifiy the end of a chain
>P1;9ANT
structureX:9ANT:FIRST :@ END : : :dros:undefined: 2.4: 0.23
RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK/
.............../
...............*

>P1;1AAA
sequence:1AAA:FIRST :@ END : : :human:undefined: 0.00: 0.00
RTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERKVKVWFQNRRMKHKRQTQ*

3. In my top file (running 8v2) include several varieties to turn het atoms on e.g
env.io.hetatom= True
SET HETATM_IO ON
io_data.hetatm = True

The script looks like this:

INCLUDE # Include the predefined TOP routines
SET ALNFILE  = 'model.ali'                    # alignment filename
SET KNOWNS   = '9ANT'                         # codes of the templates
SET SEQUENCE = '1AAA'                         # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
SET HETATM_IO on
SET STARTING_MODEL= 1                         # index of the first model
SET ENDING_MODEL  = 500                       # index of the last model
# (determines how many models to calculate)
CALL ROUTINE = 'model'                        # do homology modelling


Any help or suggestions on something I have missed would be greatly appreciated!
Elliott