> Dear Andrew and Brian!
>
> please replace BUILD_MODEL INITIALIZE_XYZ = off
> to BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD =
> 'INTERNAL_COORDINATES'
>
> in file $MODINSTALL/scripts/__generate_model.top
^^^^^^^
bin - not scripts
>
> and
> SET TOPLIB = '${LIB}/top_allh.lib'
> in your .top file.
>
> Happy landings!
>
> Yours,
>
> Azat
>
Excellent! That's certainly fixed it... But wouldn't this have been
a problem affecting everybody using Modeller for straightforward
homology modelling???
I haven't used the SET TOPLIB as I was not reading hydrogens, so it
is taking the default SET TOPLIB = '${LIB}/top_heav.lib'
I was seeing the problem with this. As far as I can see it's not
really related to the hydrogens issue. My .top file was quite simply:
INCLUDE
SET ATOM_FILES_DIRECTORY = './:/data/pdb/'
SET PDB_EXT = '.pdb'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET DEVIATION = 0
SET KNOWNS = 'xyz'
SET HETATM_IO = off
SET WATER_IO = off
SET HYDROGEN_IO = off
SET MD_LEVEL = 'refine1'
SET ALIGNMENT_FORMAT = 'PIR'
SET SEQUENCE = 'abc'
SET ALNFILE = 'align.pir'
CALL ROUTINE = 'model'
Any thoughts???
Andrew
----------------------------------------------------------------------------
Dr. Andrew C.R. Martin University College London
EMAIL: (Work) (Home)
URL: http://www.biochem.ucl.ac.uk/~martin
Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775