Re: [AMBER] Unnatural nucleic acid in DNA chain

From: Bill Ross <>
Date: Thu, 24 Jan 2019 13:15:04 -0800

In general, I'd read the paper on the ff (and earlier versions even) for
clues, and consider copying/modifying the molecule from the original
file (.prep?) including the residue in question. And when reporting an
error like this, it's easy to paste in your prep/pdb files for the
residue along with error msgs so we can see what's going on.


On 1/24/19 12:52 PM, Anthony Bogetti wrote:
> Hello,
> 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? I
> tried following the tutorial here (
> for using
> Antechamber for this, 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. Even when I
> manually add these connections into the lib file, I still get some boned
> and angle errors relating to the atom types between my two nucleotides A
> and X. Do you have any suggestions?
> Thanks,
> AB
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Received on Thu Jan 24 2019 - 13:30:03 PST
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