Hello,
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?
Thank you very much for any advice
Pavlina Slavnikova
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Received on Fri Mar 15 2024 - 08:30:02 PDT
