Re: [AMBER] residue library for na_link AmberTools19

From: David A Case <>
Date: Thu, 26 Mar 2020 08:10:41 -0400

On Wed, Mar 25, 2020, Gül Zerze wrote:
>It looks like there are major changes in nab tools in this latest version
>of AmberTools and I'm not able to find documentation on them.

Please read section 38.1 of the Reference Manual for background here. We
are indeed trying to move users away from dependence on NAB. Full
documentation is the Amber 2018 refernce manual, available at

>happy if you can guide me about how I can use nab tool of this new version
>to create random sequences of RNA (without a pdb file).

Are you looking to create "random" (single-stranded) structures? If so,
na_link would never have been a good choice, but you might want to try
RNAMake (

If you are interested in constructing helical models with varying
sequence, see Section 38.4 of the Amber 2019 Reference Manual.


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Received on Thu Mar 26 2020 - 05:30:02 PDT
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