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
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.
Missed the first question ;-) ...
There is no need to pre-align the sequences for ALIGN2D.