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
> >
> > _______________________________________________
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> > 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 - 10:00:03 PDT
