Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides

From: Elisa Pieri <elipieri.stanford.edu>
Date: Thu, 2 May 2019 22:31:19 +0000

Thanks Ilyas,

Do you have them for thymine as well?

Elisa

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________________________________
From: Ilyas Yildirim <iyildirim.fau.edu>
Sent: Thursday, May 2, 2019 2:31:36 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides

Dear Elisa,


It should exist. We have our own version of the RNA force field for all RNA residues if you are interested (5', 3', nucleotides, and nucleosides).


Best regards,


Ilyas Yildirim, Ph.D.
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________________________________
From: Elisa Pieri <elipieri.stanford.edu>
Sent: Thursday, May 2, 2019 5:10:06 PM
To: AMBER Mailing List
Subject: [AMBER] Force field for nucleobases, nucleosides and nucleotides

Hello,

I want to run MM simulations on solvated nucleobases, nucleosides and
nucleotides. I see that Amber only have parameters for nucleotides (and
with an "incomplete" phosphate group); is this correct?
Do parameters for complete nucleobases, nucleosides and nucleotides exist?
If yes, how can I access them?
I couldn't find information about this online.

Thank you!
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Received on Thu May 02 2019 - 16:00:02 PDT
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