[AMBER] RMSD of nucleic acid bases

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Fri, 18 Sep 2020 09:35:18 +0530

Dear all,

According to the tutorials on nucleic acid simulations, I am well aware of
calculating the RMSD of the nucleic acid backbone. Could someone let me
know how to calculate the RMSD of bases and the overall rmsd of my nucleic
acid simulation? For backbone rmsd, I have used the mask of P,C5' etc.
Basically if I have 20 bases in my nucleic acid, how to calculate for bases
alone and RMSD of overall structure? Thank you for any response.
Sruthi Sudhakar
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Received on Thu Sep 17 2020 - 21:30:02 PDT
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