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[modeller_usage] Help needed



Hello

I have been trying for some time now to model with 2 ligands and 1 water molecule and I feel that I have tried everything from the list, faq and tutorials and not got very far.
I have posted a number of questions to the list but can still not get this to work, properly!
I have managed to include the ligands and the water O into my output pdb by using the script and alignment below, however there is not recognition that this oxygen is a water and in the output model it is listed as BLK along with the other ligands. From reading posts in the user list I was expecting this water oxygen to be recognised as such, since i have used the w character to represent it and also HOH in the pdb file (the file has been edited to include only the protain, ligand and water that I am wishing to model around). I cannot type w at the end of the sequence alignment however as this causes modeller to fail with an out of range error.
I would really appreciate some help as I have completelty exhaused all of my options now.

Thanks
Jo

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INCLUDE
SET ALNFILE = 'CcHh1-Bamu.pap', ALIGNMENT_FORMAT = 'PAP'
SET KNOWNS = 'Bamu'
SET SEQUENCE = 'CcHh1'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET HETATM_IO = on, WATER_IO = on
CALL ROUTINE = 'model'

end of alignment (pap format) alignment
 _aln.pos  480       490       500       510       520
Bamu      RKQLPEPDLTF/..w
CcHh1     RNALPEPVIPA/...

produce model with  water included as:

HETATM 4032  O   BLK   525      37.988  89.184  33.629  1.00 25.09       2SG4034
END