building a model with water molecules.

Hi to all: About modeling with water - I tried to model a protein with water molecules that exist in the PDB file. I wrote in my TOP file: "SET HYDROGEN_IO = off, HETATM_IO = off, WATER_IO = on", replaced the word 'HETATM' with 'ATOM' in th PDB file and add to the end of the alignment, "/wwwww*" (5 molecules). But, Modeller didn't recognize the water molecules in the PDB file. the error notification was: "Number of residues in the alignment and pdb files are different: 345 340 For alignment entry: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

- the template sequance is 340 aa, and I add 5 water molecules. The PDB file containes 340 aa and 5 water molcules.

Could someone explaine me how to overcome this problem ?

thanks a lot for your help.

Moshe.

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Moshe Amitay, Bilha Fischer's lab Dept. of Chemistry Bar-Ilan University ISRAEL.