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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>
--
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 - 08:00:04 PDT
