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