building a model with water molecules.

[Moshe Amitay <>]

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.

 ---------------------------------------------------------------------

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