Regarding modeller usage - modeller_usage

25 Oct 2001


      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
this:
# 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.
from,
                                                Senthil kumar.R