[AMBER] MMPBSA's output: Which atoms are treated as Backbone Atoms (and Side Chain Atoms) for Nucleic Acids?

From: Emmanuel <emmanuel.salawu.gmail.com>
Date: Fri, 17 Nov 2017 16:22:24 +0800

Dear Amber Users,

Could you, please, kindly guide us? We want to specifically identify the
atoms that are treated as Backbone Atoms for nucleic acids when the energy
is decomposed using the energy decomposition option in MMPBSA in AMBER16.
(It is easier for us to know the backbone atoms of proteins, but there is
some ambiguity for nucleic acids.)

We are not sure whether the "backbone" in MMPBSA of AMBER16 refers to
"sugar-phosphate backbone" which is often mentioned in the literature (and
may be made up by all the atoms in the phosphate and in the sugar).

Please, kindly guide us. In MMBPSA, AMBER16, which atoms are treated as
Backbone Atoms for Nucleic Acids? We provide a sample output here

Thank you very much.

YuanTa and Emmanuel
Institute of Bioinformatics and Structural Biology
National Tsing Hua University, Taiwan
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Received on Fri Nov 17 2017 - 00:30:02 PST
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