On Mon, Mar 01, 2004 at 07:10:57AM -0800, Shamshad Zarina wrote:
> I am interested in adding ligand like glucose to one
> particular residue in my protein (which is not present
> in my template). Any ideas?
If the ligand's not present in the template, then Modeller has no way of
predicting its structure. So, you have three options:
1. Add another template which has the ligand in it, and see
http://salilab.org/modeller/FAQ.html#4
Use the BLK residue type in your alignment, and Modeller will copy the
ligand directly from the template.
2. Define topology and parameters for the ligand: see
http://salilab.org/modeller/FAQ.html#17
Use the new residue type in your alignment, and Modeller will attempt to
model the ligand using a molecular mechanics force field.
3. Add the ligand to the model after generation by hand, or using a
modeling package.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage