Re: [AMBER-Developers] Broken links in manual

From: Christina Bergonzo <>
Date: Wed, 3 Mar 2021 10:16:16 -0500

Hi Gustavo,

I still use Amber's internal programs to create NMR restraints, etc. and I
still find the NMR refinement tutorial helpful:
Things like, makeDIST_RST, makeANG_RST have still mostly worked for me
(with some library tweaking and script modifying, but I mostly do RNAs).
In some cases I gave up and wrote my own scripts to create Amber-readable
restraint files (like RDCs).
Mike Summers group released a toolkit for RNA refinement using Amber based
on this paper (, but the download
doesn't seem to exist anymore - I can send it to you (or maybe DAC knows
since he's a coauthor), but again it's RNA-focused and I am not sure how
well any of these currently work for proteins (though, if I had to guess,
everything looks better for proteins).

Hope this is helpful re: NMR refinement.

On Tue, Mar 2, 2021 at 8:08 PM Gustavo Seabra <>

> Hi All,
> I noticed that *all* links to external programs listed in page 539 of the
> Amber manual, "that can assist in preparing input for [NMR-]structure
> refinement in Amber" are broken:
> -
> -
> -
> Does anyone have up-to-date links to those programs (or something that is
> used today)?
> Best,
> --
> Gustavo Seabra.
> _______________________________________________
> AMBER-Developers mailing list

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
AMBER-Developers mailing list
Received on Wed Mar 03 2021 - 07:30:03 PST
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