[modeller_usage] help with modelling protein-DNA complex

[Elliott Stollar <>]

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