Dear Modellers,
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 ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe@itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe