You can make a RNA and then modify the backbone.

Thanks all for your answers.

The problem is Peptide nucleic acids (PNA) have different helical parameters (i.e. rise, twist etc.) than RNA. So, if I build a RNA and then modify the backbone to build PNA, it will still have all the helical parameters of a RNA.

I don't know, will that be a correct way or not?

Just use the PNA helical parameters to build the RNA. That way, the bases will be placed correctly. Then modify the backbone and minimize with restraint on the bases.

Can you suggest how to modify these backbones?

I mean is there any software or I have to do it manually ?

I couldn't find anything to build PNA. Structure files are basically text files. So, you may try to write a script to replace the atom symbols or delete some lines. For example, with a script you can delete all the lines containing information on ring oxygen and the H of the OH group; replace the atom symbol for one backbone O with N and the other with C, so on.

Thanks for your valuable suggestions.