AMBER Archive (2008)

Subject: Re: AMBER: Help...which commands in ptraj does clustering by RMSD?

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Thu Sep 11 2008 - 16:12:00 CDT

Dear Sasha,
Thanks for the saving tip!

I downloaded AmberTools and I noticed it unzips to *amber10*.
Currently, *$AMBERHOME
*points to my *amber9* directory containing not only *ptraj*, but *sander*too.
should I overwrite amber9 directory with the contents of amber10?
Unfortunately, *$AMBERHOME *can only point to a single *amberX* directory.

Also, does anyone has a feeling about timing ? How long does it take to
cluster 1000 frames ? I assume it scales with the square of the number of
frames.

Best regards,

On Thu, Sep 11, 2008 at 4:39 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:

> Jose,
> I had exactly the same problem very recently. ptraj in Amber 9 doesn't have
> this feature - you need to get AmberTools. That version has the clustering
> capability.
>
> Sasha
>
>
> Jose Borreguero wrote:
>
> Dear Amber users,
> I am reading the Amber9 manual and I can't find the ptraj command to
> cluster the frames in a trajectory by mutual RMSD. Can anyone please tell me
> what is the command?
> Many thanks
> --
> Jose M. Borreguero
> Postdoctoral Associate
> Oak Ridge National Laboratory
> P.O. Box 2008, M.S. 6164
> Oak Ridge, TN 37831
> phone: 865-241-3071 fax: 865-576-5491
> Email: borreguerojm_at_ornl.gov
>
> 

-- 
Jose M. Borreguero
Postdoctoral Associate
Oak Ridge National Laboratory
P.O. Box 2008, M.S. 6164
Oak Ridge, TN 37831
phone: 865-241-3071 fax: 865-576-5491
Email: borreguerojm_at_ornl.gov

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