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

From: David A Case <>
Date: Tue, 18 Dec 2018 12:10:33 -0500

On Tue, Dec 18, 2018, 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.

Seeing details about the exact error messages from tleap would be a big
help. But basically, the PDB file you created from Avogadro must have
a modified residue whose name matches that in the library file you
created, *and* each of the atoms in that PDB file must match an
atom name in the library file. It is quite common that you would have
to manually edit the PDB file to make sure that residue and atom names
in there match those in the libary files you are loading.

....good luck...dac

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