Re: [AMBER] RMSD of nucleic acid bases

From: Saikat Pal <>
Date: Fri, 18 Sep 2020 06:10:42 +0000 (UTC)

Dear Sruthi,
You can use ":1-20" (for all atoms) or ":1-20&!.H=" (for all heavy atoms) for the overall structure of the nucleic acid. For a specific base, u have to mention the residue with the atom name individually.

Thanks and Regards,
Saikat Pal


    On Friday, 18 September, 2020, 09:35:46 am IST, Sruthi Sudhakar <> wrote:
 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 - 23:30:02 PDT
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