Hi,
Please change the "average-linkage" in your script to "averagelinkage".
Hope it should work.
Regards
Fredrick.
Quoting moitrayee.mbu.iisc.ernet.in:
> 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
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 22 2010 - 08:30:03 PDT
