This is the cluster command I used:
trajin ../PknGAde_md_rest20ns_reimage.mdcrd
cluster out PknGAde_restr20ns representative pdb average pdb all amber averagelinkage clusters 5 rms sieve 10 :247 <:5.0
Suggestions?
vale
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: Brian Radak [radak004.umn.edu]
Sent: Wednesday, August 06, 2014 3:37 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Cluster results
I think you'll have to provide the specific cluster command you used if you
want help on this.
Also, if I remember correctly, the cluster implementations in ptraj and
cpptraj are a bit different, but the latter is still recommended.
Regards,
Brian
On Wed, Aug 6, 2014 at 8:22 AM, Valentina Romano <valentina.romano.unibas.ch
> wrote:
> Dear Amber users
>
> I clustered a MD trajectory using the command cluster in ptraj. I used 5
> as number of clusters.
>
> In addition to 5 filename.ci files (e.g. filename.c0, filename.c1 etc), I
> obtained additional files for each .ci file.
> For instance, in addition to filename.c0 I also obtained flilename.c0.1,
> filename.c0.2 and so on.
>
> Anyone can explain me what these files are?
>
> Best,
> Valentina
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
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Received on Wed Aug 06 2014 - 07:30:02 PDT
