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