You could keep a *specific number* of water molecules around each
individual peptide in your "1 peptide" trajectories by using the "closest"
command.
--Marc
On 30 January 2015 at 14:56, 浅井 賢 <suguruasai.gmail.com> wrote:
> Dear Marc,
>
> I see. Hum then what happen If I want to keep a peptide and water
> molecules (which start from residue id 501 or so on)?
> I'd like to analyze the water dynamics around each clusters as well.
> Only the way I know is to use trajectory files which produced via
> 'clusterout' option of 'cluster' command.
>
> Thanks a lot
>
> Regards
>
> Asai
>
> On 2015年01月30日 23:50, Marc van der Kamp wrote:
> > 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
> >>>>
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> >>
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Received on Fri Jan 30 2015 - 07:30:03 PST
