AMBER Archive (2008)
Subject: Re: AMBER: Help...which commands in ptraj does clustering by RMSD?
From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Sep 11 2008 - 16:48:14 CDT
In my case, I installed AmberTools in a separate directory, since I
didn't want to mess with the current working installation of Amber 9.
During the installation, I just set the environment variable $AMBERHOME
in the shell I used to do the compilation, etc. When I need to use
clustering-capable version of ptraj, I just reference it by fully
The clustering is fast. Depends on the size of the system, but shouldn't
be more than a minute for 1000 frames (typically, much less than that).
Jose Borreguero wrote:
> Dear Sasha,
> Thanks for the saving tip!
> I downloaded AmberTools and I noticed it unzips to /amber10/.
> Currently, /$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
> <mailto:obuzko_at_ucla.edu>> wrote:
> 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.
> 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 <mailto: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 <mailto:borreguerojm_at_ornl.gov>
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