Hi
I got both <filename>.rep.c<#> and <filename>.avg.c<#>. In details, I got 5 representative structures and 5 average structures ( 1 per each cluster).
Please find in attachment the ptraj output file I got.
Hope this help to understand.
Best,
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: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Wednesday, August 06, 2014 5:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Cluster results
Hi,
Just to check, did you also get files <filename>.rep.c<#> and
<filename>.avg.c<#> (for representative and average structures
respectively)? The only way I can think of you getting files named
<filename>.c<#>.X is if you chose a file format that writes multiple
frames (like Amber restart or PDB etc). I think we would need to see
your entire ptraj output to debug further.
As Brian suggested, if you're just using averagelinkage you may want
to try using cpptraj instead; it's faster and better-supported
overall.
-Dan
On Wed, Aug 6, 2014 at 8:27 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> 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,
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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- application/octet-stream attachment: ptraj.out
Received on Thu Aug 07 2014 - 02:00:02 PDT
