> 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) martin@biochem.ucl.ac.uk (Home) andrew@stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775
In general, I found it better to put the initial coordinates for inserted atoms on a line connecting the two known endpoints of the insertion (with totally unreasonable stereochemistry), rather than in an extended conformation with ideal stereochemistry. But sometimes the opposite may be true. It is the question of the optimizer in the end ...
Best, Andrej
> > > 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) martin@biochem.ucl.ac.uk (Home) andrew@stagleys.demon.co.uk > URL: http://www.biochem.ucl.ac.uk/~martin > Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775 >
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
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