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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>
--
-------------------------
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 - 07:30:02 PST
