Dear Asai,
If you strip out only one peptide (be it :1-10, :11-20, :21-30 etc.), all
the trajectories (just xyz coordinates) can be read in by first reading in
a prmtop file with only one peptide in it.
So after reading in the different trajectories in cpptraj (on top of the
prmtop file), you would only have residues :1-10.
Hope that helps,
Marc
On 30 January 2015 at 14:45, 浅井 賢 <suguruasai.gmail.com> wrote:
> Dear Marc
>
> Thanks for your suggestion. If I understood correctly, I think I need to
> re-organize residue ID of each copies in each produced trajectories to
> specify all copies in 'cluster' command with a single amber mask (e.g
> ':1-10') right? Then how can I do it? Or is it ok to specify the
> molecules as ':1-10,11-20,21-30,...' (or ':1-500') while each frames
> only have a single copy?
>
> Thanks again for your reply.
>
> Best regards
>
> Asai
>
> On 2015年01月30日 21:41, Marc van der Kamp wrote:
> > 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 30 2015 - 07:00:05 PST
