Re: [AMBER] Unnatural nucleic acid in DNA chain

From: David A Case <>
Date: Fri, 25 Jan 2019 07:53:26 -0500

On Thu, Jan 24, 2019, Anthony Bogetti wrote:
>I'm trying to run a MD simulation with a small DNA molecule that contains
>an edited nucleotide (it's basically an Adenine without the base). For
>instance, my molecule is AXA where X is just the deoxyribose sugar. How
>would you suggest going about generating force field parameters for X?

Try a google search on something like "amber DNA abasic", to find papers
where people have carried MD simulations on abasic nucleotides. A
pretty simple idea is just to remove the base from A, replacing it with
a hydrogen. I think LEaP can find all the needed parameters.

>but I'm getting errors saying I have a one-sided
>connection and related errors to this about leap not being able to find
>bond parameters for the bond between the two nucleotides.

Generally, when making a modification of an existing amino acid or
nucleotide, it is preferable to use Amber atom types and do this "by
hand", rather than to try to use antechamber and use the GAFF forcefield
for the modified residue. You can see the reason: even if you succeed,
you need to obtain parameters for bonds and angles that cross the
boundary between the Amber region (the unmodified nucleotides) and the
GAFF region (the abasic site).

...hope this helps...dac

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Received on Fri Jan 25 2019 - 05:00:02 PST
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