I would simply write out trajectories with just one copy (using the
appropriate "strip" command in cpptraj), do this for all 50 copies, and
then read in the trajectories (with ONLY your peptide, no water etc.) back
into cpptraj for clustering.
Hope this helps,
Marc
On 30 January 2015 at 12:06, 浅井 賢 <suguruasai.gmail.com> wrote:
> Dear AMBER users
>
> I'm using Amber 14 and I'm trying to cluster 50 copies of a single
> molecule (very short peptide).
> I know that I can cluster a single molecule in the trajectory via
> 'cpptraj' as:
>
> cluster clusters 10 rms :1-10 out cluster.log ...
>
> But my system has 50 copies of the molecule (:1-10, :11-20, :21-30, ...)
> and I'd like to find the difference not only between frames but also
> between these copies of each frames.
> Is there any way to do it? Any recommendations will be appreciated.
>
>
> Thanks.
>
>
> ---
> Laboratory of Plasmamembrane and Nuclear Signaling, Graduate school of
> Biostudies, Kyoto University.
>
> Suguru ASAI
>
> Tel: +81-75-753-7906
> Fax: +81-75-753-7906
> E-mail: asai.suguru.86x.st.kyoto-u.ac.jp
> URL: http://www.lif.kyoto-u.ac.jp/labs/chrom/
> Address: Room 419, Faculty of Medicine Bilding G (South Campus Research
> Bilding), Yoshida Konoemachi, Sakyo-ku, Kyoto, Japan
>
>
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Received on Fri Jan 30 2015 - 05:00:02 PST
