Re: [AMBER] Abasic Site and Leap Polymerization

From: Christina Bergonzo <>
Date: Mon, 30 Mar 2020 11:07:58 -0400


In the past (the way past - 2011!) we have used these parameters:

Kun Song created these leap files while in Carlos Simmerling's lab.
I attached the off and frcmod files to this email, as well as a picture.

Please make sure they are compatible with any changes to the DNA FF since


On Mon, Mar 30, 2020 at 10:36 AM Robert Molt <> wrote:

> 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
> clarification.
> 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.
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST

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(image/jpeg attachment: abasic-site.jpg)

Received on Mon Mar 30 2020 - 08:30:02 PDT
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