Re: [AMBER] Simulating a DNA Double helix with a mutated base pair

From: Pratul Agarwal <>
Date: Tue, 18 Dec 2018 17:07:55 +0000

Could you provide more information on what "atomtype issues" you are getting?

Obvious question -- did you make sure all atom types have been assigned for the unnatural base? What did you use to parameterize?

Also if your input PDB file has atoms named differently than the ones in loaded templates in leap, you will get messages regarding unknown atoms and missing atoms. Missing atoms can be generated by leap but unknown atoms are fatal. Have you tried making sure that the output PDB from Avogadro has same atoms names as in leap? Just something to keep in mind.

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 12/18/2018 11:43 AM, Anthony Bogetti wrote:


I'm looking to simulate a small DNA double helix with one of the base pairs
replaced with a certain small molecule. I have already parameterized the
"unnatural" base following the amber tutorials.

However, I am having trouble generating a full structure of my DNA double
helix with the small molecule attached. I've tried creating the DNA
molecule in Avogadro and then manually editing the relevant base pair, but
I get atomtype issues when trying to generate the topology files in leap.

What would be the best way to generate my DNA model with the "unnatural"
base pair? How can I do so in a way that preserved amber atomtypes (for
any forcefield; that doesn't matter at this point).

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Received on Tue Dec 18 2018 - 09:30:02 PST
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