On Fri, Mar 15, 2024, Slavnikova Pavlina via AMBER wrote:
>
>I am having problems with base-pairing in nastruct, so I would like to
>define it and keep it fixed. I have found the option '[specifiedbp pairs
><b1>-<b2>, ... ]' on AMBER-Hub (https://amberhub.chpc.utah.edu/nastruct/)
>which would be perfect for my usecase, but then I found out that it is not
>implemented in the versions I am working with (Amber18 and Amber22). The
>other possibilities (reference structure) do not seem suitable to me, as I
>will use the same pattern for multiple simulations. I have these pairing
>issues in all frames, so I really prefer to define the pairing easily in a
>residue-way like 1-66,2-65,3-64,... Please, do you know some easy way how
>to achieve that?
Update to AmberTools23(?). Using conda environments, it's pretty easy to
download the pre-built conda package for AmberTools, and only use it when
you activate the appropriate conda environment. That way, nothing should
interfere with your existing (rather out-dated) installations.
...good luck.....dac
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Received on Sat Mar 16 2024 - 12:00:02 PDT
