prasun kumar wrote: > I am trying to add two proteins by means of making bond between the > residues of both the proteins.Can we do this using modeller.

Sure - you can use the LINK patch. You can see an example using LINK at http://salilab.org/modeller/wiki/Cyclic%20protein

But note that this joins the backbones, and if that's really want you want to do it's probably easier just to stick your two PDBs together manually by editing the files with a text editor.

> this question came into my mind because of the DISULFIDE bond that we > can make using modeller.

If you want to make some other kind of linkage between the two proteins, you would need to add your own patching residue type for the linker. Modify top_heav.lib accordingly using the DISU or LINK patches as examples and see FAQ question #9. You may also need to edit par.lib to define suitable parameters for any new bonds or angles added by your patch.

Ben Webb, Modeller Caretaker