Andrew Martin wrote:
>
> > 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 agree it would be a problem to everybody trying to use explicit
hydrogen modelling. I am sure it will be fixed in next versions. At
least now after creating this mail list subscribed users could patch
their modeller versions.
> 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, could you please send directly to me align.pir and file with
template coordinates if it is not in PDB.
Regards,
Azat.
--
- Dr. Azat Badretdinov
- The Rockefeller Univ, Box 270
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail:
- WWW/URL: http://salilab.org/~azat