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Can anyone please tell me… How to make index file indicating only Nitrogen bases of the RNA… Since, manually its too time consuming process…
Use make_ndx and specify a N* to get all the nitrogens (the only N atoms in RNA are in the bases, anyway).
Sorry sir I wasn’t able to specify correctly… Actually … I was talking about 4 nitrogenous bases of RNA (A,U,G,C)… Can I make index file of all carbons, nitrogen and oxygen atoms of these bases… Please help me with it…
I got it now… Thank you soo much for the hint…
I used make_ndx command and then typed: r N* O* C*…It created a new group 9 for all the nitrogenous bases…
If you want all the atoms in the bases, the easiest way is to create groups that define the sugar-phosphate groups and then save the complement, e.g.
> a *P* | a *'* > (this creates a new group, let's call it X) > ! X > (this is a group that will contain the base atoms, but definitely verify its contents)
okk… thank you soo much…