The version of AmberTools that I use is Version 1.5 . So I think I can sovle the problem now.
Thank you again.
-Sun
At 2012-12-21 11:54:26,"Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>What version of cpptraj are you using? It should be the fully updated
>AmberTools 12 version.
>
>-Dan
>
>On Thursday, December 20, 2012, Sun wrote:
>
>> Hello Dan,
>>
>> I am very appreciated for you help. I tried a new cluster analysis using
>> the cpptraj clustering with the keyword "nofit" according to your advice.
>> But it seemed not to work. When I runned the command line " cpptraj lig.top
>> trajin ", it gave me following message:
>> .....
>> Read 1490 frames and processed 1490 frames.
>> OUTPUT:
>> DATASETS:
>> There are no data sets.
>> NO DATASETS WILL BE OUTPUT
>>
>> Actually.the trajin file that I used this time is amost the same as the
>> first ptraj run except the last command action "cluster". I did use the
>> command line that you recommend . I also checked the Amber Tools manual for
>> detail information about cpptraj clustering, it seems strange that cpptraj
>> does not contain such a cluster action . Is there something that I
>> misunderstand ?
>>
>>
>> Sincerely,
>> BIn Sun
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> At 2012-12-20 23:22:27,"Daniel Roe" <daniel.r.roe.gmail.com <javascript:;>>
>> wrote:
>> >Hi,
>> >
>> >Unfortunately I don't think there is an option to turn off RMS-fitting in
>> >ptraj clustering. However there is an option to do it in cpptraj via the
>> >'nofit' keyword. Be aware however that clustering in cpptraj has slightly
>> >different syntax, options, and output. Based on the input you provided I
>> >would recommend:
>> >
>> >cluster nofit mass clusters 8 out cnumvtime.dat averagelinkage summary
>> >ligand.summary.dat info ligand.info.dat clusterout ligand.nc clusterfmt
>> >netcdf repout rep.ligand repfmt pdb
>> >
>> >This will cluster using no-fit RMS (mass-weighted), final target 8
>> clusters
>> >using average linkage hierarchical agglomerative clustering. Afterwards,
>> >'cnumvtime.dat' will contain cluster # vs frame, 'ligand.summary.dat' will
>> >contain some data on each cluster, 'ligand.info.dat' will show cluster
>> >populations in a ptraj-like format, 'ligand.nc.cX' will contain all
>> frames
>> >for cluster X in netcdf format, and rep.ligand.X.pdb will contain a
>> >representative structure for cluster X in PDB format. There is no
>> 'average'
>> >keyword, but you can get the average of a cluster by reading in one of
>> the '
>> >ligand.nc.cX' trajectories and using the 'average' command. See the
>> manual
>> >for more details.
>> >
>> >Hope this helps - let me know if you have any more questions.
>> >
>> >-Dan
>> >
>> >On Thu, Dec 20, 2012 at 1:38 AM, Sun <sunbintyy.163.com <javascript:;>>
>> wrote:
>> >
>> >> Dear all,
>> >> I have about 1500 conformers which were generated by a docking
>> calculation
>> >> of a ligand. These conformers were distributed at different positions
>> in
>> >> the active site of the receptor. And I used ptraj to do cluster analysis
>> >> for these conformers. But when I checked the results of the cluster
>> >> analysis, I found that all the 1500 conformers were about at the same
>> >> position. I inferred that cluster analysis does alignment first and then
>> >> groups conformers . So I wander if cluster analysis does really do
>> >> alignment firstly ? and if it does , is there anyway to turn off the
>> "do
>> >> alignment" option ?
>> >>
>> >> Here is the trajin file:
>> >> trajin ligand1.pdb
>> >> trajin ligand2.pdb
>> >> trajin ligand3.pdb
>> >> .....
>> >> trajin ligand1490.pdb
>> >> cluster out ligand representative pdb average pdb all pdb averagelinkage
>> >> clusters 8 rms mass
>> >>
>> >> Many thanks for your help
>> >> Bin Sun
>> >>
>> >> _______________________________________________
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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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>>
>
>
>--
>-------------------------
>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 Dec 20 2012 - 20:30:03 PST
