2 problems - HETATM_IO and strange log (fwd)

[Frank J A B <>]

Dear All

I'm facing to problems with modeller.
In the FAQ's question #16 there is an explanation on how to use hetero
atoms in modelling adding the line HETATM_IO = on in the top script.
There is also a comment (confuse in my opinion) about the use of w for
water and . for other atoms in the alignment that still remains unsolved
to me. In my case I'm trying to use FAD in the modelling.
I can't wonder how to edit the alignment to include this Ws and .s
Check the example given.

INCLUDE     
SET ALIGNMENT_FILE = 'align1.ali', KNOWNS='templ1', SEQUENCE='targ1'
SET HETATM_IO = on, WATER_IO = on
CALL ROUTINE = 'model'

The alignment file:
     
>P1;templ1
structureX:templ1:1::10::
FAYVI/.wwww*
     
>P1;targ1
sequence:targ1:1::8::
-GWIV/.ww-w*

Need I to repeat the entire alignment (template/target) inside the same
.pir file, but now only with signs like - , ., w , #) where
the .s/Ws positions correpond to those aa that make contact with the
HETATM in the structure/template ?

The second question is about my log file. 
I'm habituated to use regularly Modeller since version 4 but suddenly the
job was finished abruptly with this :


                         MODELLER 6v2, 17 Feb 2002
     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

assgn___544E> Variable name not recognized:
/pipe1/databases/pdb/uncompressed_files/pdb1hci.ent
              Command line:  INCLUDE 
assgn___525E> Error in TOP variable assignment. 
recover____E> ERROR_STATUS >= STOP_ON_ERROR:  1   1 


Is this some kind of bug or a user error ?
I'm sure that the files are typed correctly (case-sensitive) and the
folder where the job is started has all the files in it.

Any hint asap will be very much appreciated.

Thanks in advance
brgds

Frank Alarcon
LNCC - Brasil
www.lncc.br