On Tue, Sep 19, 2023, Fadaei Fatemeh Mgr. via AMBER wrote:
>
>I am writing to seek assistance with an issue I have encountered while
>using AmberTools23 on my Ubuntu 23.04 system. Specifically, I am
>experiencing problems with the 'nab' command, which does not seem to work
>as expected.
The nab program has been removed from AmberTools starting (I think) with
AmberTools23. This is old code, and both primary authors are now retired.
This code was "deprecated" about 6 years ago, and was removed from the
Reference Manual about then as well. With AmberTools23, we stopped
including the (now undocumented) code.
If you wish to use nab, grab an older version from conda-forge, e.g.
> conda create --name AmberTools22
> conda activate AmberTools22
> conda install -c conda-forge ambertools=22
[I think(?) AmberTools22 still has NAB.] Getting help will probably require
finding volunteers on the mailing list that are familiar with how NAB might
be used to build unusual-shape DNA.
Notes for others:
Many of the features of NAB are now in AmberTools/nabc, which has
much of the force-field based functionality of NAB, but without the
NAB language itself. See the Reference Manual for more info.
...dac
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Received on Wed Sep 20 2023 - 10:00:02 PDT
