Hello<br>
<br>
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. <br>
I have posted a number of questions to the list but can still not get this to work, properly!<br>
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.<br>
I would really appreciate some help as I have completelty exhaused all of my options now.<br>
<br>
Thanks<br>
Jo<br>
<br>
top<br>
INCLUDE<br>
SET ALNFILE = 'CcHh1-Bamu.pap', ALIGNMENT_FORMAT = 'PAP'<br>
SET KNOWNS = 'Bamu'<br>
SET SEQUENCE = 'CcHh1'<br>
SET STARTING_MODEL = 1<br>
SET ENDING_MODEL = 1<br>
SET HETATM_IO = on, WATER_IO = on<br>
CALL ROUTINE = 'model'<br>
<br>
end of alignment (pap format) alignment<br>
&nbsp;_aln.pos&nbsp; 480&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
490&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
500&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
510&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 520<br>
Bamu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RKQLPEPDLTF/..w<br>
CcHh1&nbsp;&nbsp;&nbsp;&nbsp; RNALPEPVIPA/...<br>
<br>
produce model with&nbsp; water included as:<br>
<br>
HETATM 4032&nbsp; O&nbsp;&nbsp; BLK&nbsp;&nbsp;
525&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 37.988&nbsp; 89.184&nbsp;
33.629&nbsp; 1.00 25.09&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2SG4034<br>
END<br>
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