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

From: Kenneth Huang <>
Date: Tue, 12 May 2020 17:06:34 -0400


Thanks for the info! I figured it was a very long shot given how long ago
it was. I'll try out the position swap, though out of curiosity is there
any reason why I wouldn't use the adenosine from DNA.OL15 instead of an RNA



On Mon, May 11, 2020 at 9:13 PM David A Case <> wrote:

> 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
> >unpublished
> >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.
> ....dac
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Received on Tue May 12 2020 - 14:30:02 PDT
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