Dear All
I'm facing two 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 (not clear to me) about the
use of Ws for water and .s for other atoms in the alignment that still
remains unsolved to me.
In my case I'm trying to use FAD during the modelling.
I can't wonder how to edit the alignment to include this Ws and .s
I understand that the backslash is a sequence break, but I deduce (not
sure) that you must to repeat for each residue a symbol like w, . or
whatever in the same .pir file after the backslash. I didn't find any
explanation along the manual regard this.
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 using only signs like - , ., w , #) where
the .s/Ws positions correpond to those aa that make contact with the
HETATM in the 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 (the tops, ali
and pdb files).
I'm not using any file located in the path shown above :
/pipe1/databases/pdb/uncompressed_files/pdb1hci.ent
Any help will be welcome
Thanks in advance
Frank Alarcon
LNCC - Brasil
www.lncc.br