Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides

From: David A Case <>
Date: Fri, 3 May 2019 09:40:36 -0400

On Thu, May 02, 2019, Elisa Pieri wrote:
>I want to run MM simulations on solvated nucleobases, nucleosides and
>nucleotides. I see that Amber only have parameters for nucleotides (and
>with an "incomplete" phosphate group); is this correct?
>Do parameters for complete nucleobases, nucleosides and nucleotides exist?
>If yes, how can I access them?

Section 3.2.3 in the Amber reference manual shows you how to construct
nucleosides and nucleotides using our recommended force fields.

I'm not sure what you mean by "complete nucelobases". Models for the
bases usually (but not necessarily) replace the C1' carbon of the sugar
with a methyl group. You'd have to construct these by hand: go into
xleap, remove everything beyond C1' (towards the backbone), add in three
hydrogens to make the methyl group. Assign atom types for the methyl,
and adjust its charges to get a neutral molecule.

...good luck....dac

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Received on Fri May 03 2019 - 07:00:02 PDT
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