Re: [AMBER] Cluster results

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Thu, 7 Aug 2014 08:34:00 +0000

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, > Department of Chemistry : Piscataway, NJ > 08854-8066 > radak004@umn.edu : > ==================================================================== > _______________________________________________ > 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 -- ------------------------- 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 (801) 585-6208 (Fax) _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Thu Aug 07 2014 - 02:00:02 PDT
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