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> 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> 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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Received on Thu Dec 20 2012 - 20:00:03 PST
