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

From: Anthony Bogetti <anthony.bogetti.gmail.com>
Date: Tue, 18 Dec 2018 11:43:11 -0500


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 - 09:00:04 PST
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