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 - 17:01:02 CDT

Great...thanks!

On Thu, Sep 11, 2008 at 5:48 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:

> Jose,
> 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 $AMBERHOME in the shell I
> used to do the compilation, etc. When I need to use clustering-capable
> version of ptraj, I just reference it by fully qualified path.
>
> The clustering is fast. Depends on the size of the system, but shouldn't be
> more than a minute for 1000 frames (typically, much less than that).
>
> Sasha
>
>
> Jose Borreguero wrote:
>
> Dear Sasha,
> Thanks for the saving tip!
>
> I downloaded AmberTools and I noticed it unzips to *amber10*. Currently, *$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> 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
>
> 

-- 
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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