I want to read in atomic coordinates and use modeller to perform
MD on the system. In general, I can do this. But I also want to restrain
the atoms in the file so that it holds its shape to some extent. So I make
a copy of the file and read it in as:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
SET ALNFILE = '/Applications/modeller6v2/ALIGN.ali' # alignment filename
SET KNOWNS = 'molecule_copy'
SET SEQUENCE = 'molecule' # code of the target
SET ATOM_FILES_DIRECTORY = '/Applications/modeller6v2/atom_files'
READ_MODEL FILE = 'molecule.pdb', GENERATE_METHOD = 'read_xyz'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
So now I thought that the easiest way to restrain my model to the original shape
was to make homology derived restraints using:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = on
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
But I am having an awful time, and I think that I am not defining segments
correctly (if at all). I get the following error:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
make_re_417_> Restraint type to be calculated: distance
make_re_477E> No templates in the alignment.
Number of sequences in the alignment:
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Do I need to define my template/known structure more than what is shown
above? I have looked through 'homcsr' for ideas, but I couldn't figure it out.
Any help would be grateful,
Michael
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Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143