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 >