You probably did not add the ligand to your alignment, only residues
that are defined in the alignment will appear in the model. The easiest
way to do this is by using a "block" residue to represent your ligand.
You can check FAQ #16 in the modeller manual and section 2.2.1 of the
manual for an example and details on block residues.
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
R Senthil Kumar wrote:
> Dear friends,
> I am Ph.D student doing my work in the field of protein modelling in
> Center for DNA Fingerprinting & Diagnostics(CDFD),Hyderabad,India.
> I am having some doubts about Comparative modelling using modeller
> package.Kindly i request you to clear my doubts.
> 1.First thing is before submitting to align2D for alignment the sequences
> in the ali file whether it has to be aligned by some sequence alignment
> program like clustalW or we can submit the the raw sequence in PIR format
> in the ali file to align2D.top file?.
> 2. I am taking three templates for homology modelling for my model.And
> one of my template has hetroatoms like glucose(ligands) and i want to
> include those hetroatoms to my model.For that i changed my model.top like
> # Homology modelling by the MODELLER TOP routine 'model'.
> INCLUDE # Include the predefined TOP routines
> SET ALNFILE = 'align2d.ali' # alignment filename
> SET KNOWNS = '1hkca1' '1hkca2' '1bdg' # codes of the templates
> SET SEQUENCE = 'ppgk' # code of the target
> SET ATOM_FILES_DIRECTORY = './' # directories for input atom files
> SET STARTING_MODEL= 1 # index of the first model
> SET ENDING_MODEL = 20 # index of the last model
> SET HETATM_IO = ON
> CALL ROUTINE = 'model' # do homology modelling
> But it is not including the hetroatoms in the model.I don't know
> why?.Plese help me in this regard.
> Senthil kumar.R