Hi Gustavo,
I still use Amber's internal programs to create NMR restraints, etc. and I
still find the NMR refinement tutorial helpful:
http://ambermd.org/tutorials/advanced/tutorial4/index.php
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 (
https://pubmed.ncbi.nlm.nih.gov/20549304/), 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.
-Christina
On Tue, Mar 2, 2021 at 8:08 PM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> 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:
>
> - http://ambermd.org/sane.zip
> - http://garbanzo.scripps.edu/nmrgrp/wisdom/pipe/tips_scripts.html.
> - http://picasso.ucsf.edu/mardihome.html
>
> Does anyone have up-to-date links to those programs (or something that is
> used today)?
>
> Best,
> --
> Gustavo Seabra.
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Wed Mar 03 2021 - 07:30:03 PST
