Hi,
Someone more familiar with the clustering code may want to correct me,
but I'm not sure this is possible. The cluster command automatically
does best-fit RMSD and I don't think there is an option to turn that
off or provide separate fit and calculation masks.
-Dan
On Wed, Jun 22, 2011 at 7:21 AM, Katrine Kirkeby Skeby <kks.chem.au.dk> wrote:
> Hi
>
> I was wondering if you can align your structure by e.g. c-alphas and
> then cluster by the rmsd of a ligand using the ptraj cluster command?
> Or are you forced to use the same selection for alignment and
> clustering?
>
> Thank you in advance.
>
> /Katrine Skeby
> PhD-student
> Biomodelling Group
> Department of Chemistry
> Aarhus University
> Office 1510-421
> Tlf. +45 5073 4985
>
>
>
>
>
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Received on Mon Jun 27 2011 - 22:30:03 PDT
