[AMBER] Nastruct reference file format

From: Robert Molt <rwmolt07.gmail.com>
Date: Tue, 1 Jun 2021 16:58:12 -0400

Good evening,

I am confused for the format of custom nucleic acid in cpptraj analysis.
On page 687 of the 2020 manual, one can see the input file format. On
the second line, one sees

G G G5 G3

The manual states that these are:

"used to identify the underlying base type...if none of these, it will
be considered an unknown residue (which just means WC hydrogen bonding
will not be identified)"

I am unclear on what is being said here. Can further explanation be offered?

1.) "Underlying" meaning the custom nucleic acid is "most like" one of
the traditional nucleic acids? If so, what defines this property? In my
case, I have custom nucleic acids which are pretty different from the
natural nucleic acids. In fact, in one case, I have an amino acid which
has inserted into a DNA helix to replace a nucleic acid (poorly).

2.) What do "G G G5 G3" signify, in the example of guanine? What do each
of the letters/numbers indicate?

Dr. Robert Molt Jr.
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Received on Tue Jun 01 2021 - 14:00:02 PDT
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