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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--
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Department of Medicinal Chemistry
University of Utah
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Received on Wed Oct 17 2012 - 13:30:06 PDT
