Hi Raag,

you can modify the structure at C-terminus or place like a particular sidechain group, N-terminus, etc using Chimera. Also, there are commercial softwares like Sybyl-X-2.1, Discovery Studio-4.5, Schrodinger, which may help you in modifications.

I agree with Tanuj Sharma. There are some software, such as Discovery Studio, Chimera, and others, in which you can add modifications at protein terminals. However, if you want to see the modification happening, it is needed to use a quantum chemistry method.

hi Raag,

Quantum chemistry method, as suggested by Jose Xavier, will definitely provide valuable insights how the Terminal residues are modified and which modification is energetically more favorable. You can use Gaussian, or any other software for quantum studies. 

but, only use the part of terminal residues for studies, as these methods require lot of time if the system the complex.

hello everyone... can anybody guide me how to apply or add specific molecules to PDB file using Discovery Studio or Chimera in order to apply PTMs.. Thanks and have a nice day