Hello,
Clustering is detailed in the AmberTools manual (see page 113 of the version
1.4 manual). It'll tell you how to use it in there. I've never used it
myself.
All the best,
Jason
On Fri, Oct 8, 2010 at 12:55 PM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Jaxel,
>
>
>
> Thank you very much. I have done the analysis for last snapshot already.
>
>
>
> How about clustering? What is the command needs to be use to do clustering
> with ptraj?
>
>
>
> Many thanks,
>
>
>
> CAt
>
> > Date: Fri, 8 Oct 2010 10:50:48 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] How to convert mdcrd to pdb for display?
> >
> > Hello,
> >
> > Clustering may help you pick out representative structures. As for
> printing
> > out a PDB of the last step, that's quite simple. Consider an example
> where
> > you have 1000 frames. The ptraj script below will do what you describe:
> >
> > trajin my_trajectory.mdcrd 1000 1000 1
> >
> > trajout my_snapshot.pdb pdb
> >
> > Good luck!
> > Jason
> >
> >
> > On Fri, Oct 8, 2010 at 10:46 AM, Catein Catherine <
> askamber23.hotmail.com>wrote:
> >
> > >
> > > Dear Sir/Madam,
> > >
> > >
> > >
> > > I would like to convert the trajectory final structure to PDB format. I
> > > notice that if I do the ptraj average, the structure of some of the
> flexible
> > > part of the structures will become strange.
> > >
> > >
> > >
> > > I am writing to ask if there are any good display the representative
> > > structure after a MD structure.
> > >
> > >
> > >
> > > What is the ptraj command that we should use to include only one step
> of
> > > the trajectory to a PDB file, e.g. the structure of the last step?
> > >
> > >
> > >
> > > Catherine
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 08 2010 - 11:30:04 PDT
