**1. To get the list of base pairs which are protonated **

**2. To get the list of base pairs which show amino acceptor interactions**

**3. To get the list of base pairs, involving water molecule (water mediated optimized geometry)**

**4. To get the list of base-pairs which are not observed in nature but considered for geometry optimization by modelling the structure**

**4. To get the list of base-pairs where contrained have been usede during optimization**

RNABP COGEST version 1.0 © CCNSB, IIIT Hyderabad 2014