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