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