Hi,
You may want to try and upgrade to ptraj from AmberTools12. There have
been a few bug fixes to the clustering code since Amber11.
Also, I just noticed you specified '*****' as the argument to 'out'.
If this is the case (and not just a placeholder for a filename) this
will probably not work - you need to give a valid filename.
-Dan
On Thu, Oct 18, 2012 at 1:38 AM, Esam Tolba <eatolba.gmail.com> wrote:
> I am using ptraj and Amber 11
> *Best Regards,
> Esam
> *
>
>
> On Wed, Oct 17, 2012 at 10:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Are you using ptraj or cpptraj? Also, what version of AmberTools do you
>> ahve?
>>
>> -Dan
>>
>> On Wed, Oct 17, 2012 at 1:49 PM, Esam Tolba <eatolba.gmail.com> wrote:
>> > Thanks for the note
>> > I am using the this command for clustering
>> > cluster out ***** representative pdb average pdb averagelinkage clusters
>> 5
>> > rms
>> > I got as output three files for each cluster but the average and the
>> > represintative files are empty and there is no error in the output file
>> > *Best Regards,
>> > Esam *
>> >
>> >
>> > On Wed, Oct 17, 2012 at 3:26 PM, David A Case <case.biomaps.rutgers.edu
>> >wrote:
>> >
>> >> On Wed, Oct 17, 2012, Esam Tolba wrote:
>> >>
>> >> > > See the 'cluster' command for ptraj or cpptraj. Note that currently
>> >> > > ptraj clustering has far more options than cpptraj. Refer to the
>> >> > > AmberTools manual for more details.
>> >>
>> >> > How to use the 'cluster' command?
>> >> > and what would be the output files?
>> >>
>> >> We expect users to invest a fair amount of effort before asking people
>> on
>> >> the
>> >> list to spend their time in replies. People are willing to help for
>> >> reports
>> >> like "I read Section xxx of the manual, but I don't understand this
>> >> sentence...", or "I tried the following calculation, but I got a strange
>> >> result....". [Even better is with the addition: "I searched the Amber
>> mail
>> >> archives and Googled the error message, but could not find the help I
>> >> needed."]
>> >>
>> >> Just asking people on the list to tell you what is already in the
>> Reference
>> >> Manual is not a good use of anyone's time.
>> >>
>> >> ...dac
>> >>
>> >>
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>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
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>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Oct 18 2012 - 09:00:04 PDT
