Hello

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.

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

Option 1:
remove water_io command from top file,
try X for water and not w therefore at end of alignment
structure = /..W
and seqeunce = /...

this gives this error:
rdabrk__290E> Number of residues in the alignment and  pdb files are different:      517      516
              For alignment entry:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Option 2:
water_io = on in top file, in alignment file, structure end aligmment = /..X seqeunce end alignment = /...
gives this error
rdabrk__291E> Sequence difference between alignment and  pdb :

   STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
           1     517        24     UNK       28   TIP3  LTF..X
check_a_337E> Structure not read in:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Option 3:
water_io = on in top file, end of alignments, strcuture = /..w seqeunce = /...

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.

Option 4:
water_io = on in top file and end os alignments strcuture = /..w  seqeunce = /..w
This once agaian produces the out of range error
delete__443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    51247    47550
nselat__596E> Atom index is out of range (iatm,natm):     4033     4032
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Any help would be greatly apprecaited.

Thanks
Jo