Re: [AMBER] 2 aminpurine parameter from Bryce reference?

From: David A Case <>
Date: Mon, 11 May 2020 21:12:43 -0400

On Mon, May 11, 2020, Kenneth Huang wrote:
>This might be a long stretch, but I was wondering if anyone here had
>any insight or idea of how the 2 aminopurine parameters from the Bryce
>parameter database was generated? The reference has only listed Dr. Case
>as below-
>D.A. Case
>2-amino purine

Sorry, I have no records left of this. I'm assuming I just started with
adeninosine, and moved the amino group from the 6-position to the
2-position. Note that charges, LJ parameters and bonds/angles/torsions
for the bases are little changed from what was available in 1999. So
you could start with RNA.OL3 adenosine, do the same 6-2 position swap,
and have a "modern" version. (This assumes you want more than just the
base, i.e. that you want to incorporate 2-amino-purine into an RNA or
DNA oligonucleotide.


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Received on Mon May 11 2020 - 18:30:02 PDT
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