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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:;>
> >> 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)
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org <javascript:;>
> >http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
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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 Dec 20 2012 - 20:00:03 PST
