Hi
cluster out testcluster representative pdb \
average pdb average-linkage clusters 5 rms .CA
*remove the dash between average-linkage and it should work fine
*cluster out testcluster representative pdb \
average pdb averagelinkage clusters 5 rms .CA
*
Good luck
*
On Tue, Jun 22, 2010 at 9:56 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am trying to use the clustering algorithms in ptraj to cluster MD
> trajectories. I am using the following script: (as given in the manual)
>
> #!/bin/sh
>
> /soft/amber11/exe/ptraj 2zni.prm.top << EOF
>
> trajin /mnt/disk/rad_gyr_dhpylrs/sys0/CRD/2zni.0030_0040.crd
> trajin /mnt/disk/rad_gyr_dhpylrs/sys0/CRD/2zni.0040_0050.crd
>
> cluster out testcluster representative pdb \
> average pdb average-linkage clusters 5 rms .CA
>
> I get a warning as pasted below:
>
> PTRAJ: cluster out testcluster representative pdb average pdb
> average-linkage
> clusters 5 rms .CA
> WARNING in ptraj(), cluster: Unknown clustering algorithm!
> [No output trajectory specified (trajout)]
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 470 frames.
> Summary of I/O and actions follows:
> and so on...
>
> Please suggest me where I am going wrong.
>
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee
>
>
>
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--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jun 22 2010 - 07:30:03 PDT
