Re: [AMBER] tinker_to_amber force fields

From: David A Case <>
Date: Wed, 22 Jul 2020 15:24:37 -0400

On Wed, Jul 22, 2020, Kliuchnikov, Evgenii wrote:
>I am trying to do MD simulation of RNA with Amoeba force filed, but
>I can't generate prmtop file for that. The process ends with the
>no success getting Atom Type Definition Parameters
>when I use amoebabio09 or amoebabio18

Can you make a small test case, and post the intermediate files (.xyz and

>My question is, what actual force fields are used in tinker_to_amber (I
>mean both, Amber and Amoeba)? And is it possible that tinker_to_amber
>just does not support RNA?

tinker_to_amber doesn't use any "Amber" force field. It just refomats the
information in the analyze.out file to put into Amber's prmtop format.
Unfortunately, it's a fragile conversion, so that changes in what tinker's
anayze program writes out might well break it.

Start small: run just a short peptide (no ions,water,etc). Then just an RNA
with 2-3 nucleotides. You might need to contact Andres Cisneros at UNT --
I'm not sure that his group follows the Amber mailing list.


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Received on Wed Jul 22 2020 - 12:30:07 PDT
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