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: azat@salilab.org - WWW/URL: http://salilab.org/~azat