On 9/29/21 4:28 PM, Rana Rehan Khalid wrote: > I have a nucleotide Adenine (please see figure) I want to model it on > the particular atomic position of DNA, can I do it in the modeler. I > mean can the modeler generate the model in which I have both input > files. Please guide me if any ideas thanks.

Modeller does comparative modeling of proteins, i.e. amino acids, not nucleic acids. Although if you have DNA/RNA in your template structure, Modeller can copy it from template to model and restrain it to preserve any protein contacts, just like any other ligand. See https://salilab.org/modeller/10.1/manual/node18.html

Ben Webb, Modeller Caretaker