Re: [AMBER] cpptraj and nastruct

From: Daniel Roe via AMBER <>
Date: Mon, 26 Jun 2023 08:51:40 -0400


What version of cpptraj are you using? If it's before version 6.18.0
you should upgrade - base pair detection has been greatly improved
since then (see


On Mon, Jun 26, 2023 at 12:36 AM Jing Qu via AMBER <> wrote:
> Dear all,
> I'm using CPPTRAJ to analyze simulations of parallel strand DNA and want to
> get step parameters via nastruct. Does anyone know how nastruct identify
> the molecule as parallel strands? If I write "guessbp bptype para" in the
> nastruct command, the program will simply get stuck and look as if it is
> not continuing to run at all. If I just write "guessbp", it would seem to
> treat the molecule as anti-parallel. What is the correct way to do that?
> Thanks in advance,
> Jing
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Received on Mon Jun 26 2023 - 06:00:03 PDT
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