Hi Jing,
AmberTools23 is now available, which consists cpptraj and pytraj and other major codes. [
https://ambermd.org/GetAmber.php#ambertools]
Download Amber MD<
https://ambermd.org/GetAmber.php#ambertools>
Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids
ambermd.org
Also, you can find useful information on using cpptraj in github. [Home · Amber-MD/cpptraj Wiki (github.com)<
https://github.com/Amber-MD/cpptraj/wiki>]
[
https://opengraph.githubassets.com/4df6e4d603a0d15f353acfe21eb04ced3d48cbea3897d2430c8c4c0481b2ac67/Amber-MD/cpptraj]<
https://github.com/Amber-MD/cpptraj/wiki>
Home<
https://github.com/Amber-MD/cpptraj/wiki>
Biomolecular simulation trajectory/data analysis. Contribute to Amber-MD/cpptraj development by creating an account on GitHub.
github.com
Hope this helps.
Regards,
Zijian
________________________________
发件人: Jing Qu via AMBER <amber.ambermd.org>
发送时间: 2023年6月27日 11:57
收件人: Daniel Roe <daniel.r.roe.gmail.com>
抄送: AMBER Mailing List <amber.ambermd.org>
主题: Re: [AMBER] cpptraj and nastruct
Hi,
On one computer the version is V18.01, another one is V5.1.0. Neither one
is okay, is it? By the way, how to upgrade the cpptraj?
Thanks,
Jing
On Mon, Jun 26, 2023 at 8:51 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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 https://github.com/Amber-MD/cpptraj/pull/1018).
>
> -Dan
>
> On Mon, Jun 26, 2023 at 12:36 AM Jing Qu via AMBER <amber.ambermd.org>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 27 2023 - 19:30:03 PDT
