> 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