[AMBER] Abasic Site and Leap Polymerization

From: Robert Molt <rwmolt07.gmail.com>
Date: Mon, 30 Mar 2020 10:35:44 -0400

Good morning,

I am attempting to simulate abasic DNA with a protein "bonded" to said
DNA structure. In particular, an amino acid ends up "occupying" the
"empty" location of the abasic DNA.

In attempting to figure out the best way to construct this in Amber, I
found the following post:


in which Dr. Case elaborates that one might "remove the base from A,
replacing it with a hydrogen."

I think I have a misunderstanding of how leap works for which I seek

I have a "residue" named 48Z which is the phosphate backbone in my
crystal structure associated with the abasic site. I think I have to
"name" this residue something akin to "DA" or "DC" in order to tell leap
to connect the phosphate backbone properly (it expects to connect the
polymer). But to my understanding, the act of doing so will
automatically tell leap to fill in the missing heavy atoms? This seems
to be the behavior when I attempt this.

Dr. Robert Molt Jr.
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Received on Mon Mar 30 2020 - 08:00:02 PDT
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