Hello<br>
<br>
Many thanks for the advice Walid, I have done as you have suggested and
have made some progress but still am not seeing the behaviour that I am
expecting.<br>
<br>
I have been using the pap format for the alignment as this has being
working better and have tried the following varied options in the top
and align files, I should also mention that in my pdb i have the exact
number of ligands(2), and single water that i would want to include in
my model<br>
<br>
Option 1: <br>
remove water_io command from top file, <br>
try X for water and not w therefore at end of alignment <br>
structure = /..W <br>
and seqeunce = /...<br>
<br>
this gives this error:<br>
rdabrk__290E&gt; Number of residues in the alignment and&nbsp; pdb
files are different:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
517&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 516<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
For alignment entry:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
recover____E&gt; ERROR_STATUS &gt;=
STOP_ON_ERROR:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
<br>
Option 2:<br>
water_io = on in top file, in alignment file, structure end aligmment = /..X seqeunce end alignment = /...<br>
gives this error<br>
rdabrk__291E&gt; Sequence difference between alignment and&nbsp; pdb :<br>
<br>
&nbsp;&nbsp; STRUCTURE RES_IND&nbsp; ALN_ITYP&nbsp; ALN_RES&nbsp; X_ITYP&nbsp; X_RES&nbsp; -----*-----<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1&nbsp;&nbsp;&nbsp;&nbsp; 517&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
24&nbsp;&nbsp;&nbsp;&nbsp; UNK&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
28&nbsp;&nbsp; TIP3&nbsp; LTF..X<br>
check_a_337E&gt; Structure not read in:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
recover____E&gt; ERROR_STATUS &gt;=
STOP_ON_ERROR:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
<br>
Option 3:<br>
water_io = on in top file, end of alignments, strcuture = /..w seqeunce = /...<br>
<br>
This combination creates a model but there is no mention in the logfile
of the BLK residues or of whether the water is accepted and in the
final model the water O is written as a BLK residue. From previoud
posts i was expecting a message in the log file re the TIP3 water and
also for the model to contain a HOH or OH2 and not a BLK.<br>
<br>
Option 4: <br>
water_io = on in top file and end os alignments strcuture = /..w&nbsp; seqeunce = /..w<br>
This once agaian produces the out of range error<br>
delete__443_&gt; Restraints marked for deletion were removed.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Total number of restraints before, now:&nbsp;&nbsp;&nbsp;
51247&nbsp;&nbsp;&nbsp; 47550<br>
nselat__596E&gt; Atom index is out of range (iatm,natm):&nbsp;&nbsp;&nbsp;&nbsp; 4033&nbsp;&nbsp;&nbsp;&nbsp; 4032<br>
recover____E&gt; ERROR_STATUS &gt;=
STOP_ON_ERROR:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
<br>
Any help would be greatly apprecaited.<br>
<br>
Thanks<br>
Jo<br>