Hi Dan,
Thanks for the reply.
The exact version is
CPPTRAJ: Version V15.00
I will try the latest version.
Best Regards,
Subha
On Tue, Jun 26, 2018 at 11:53 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hm - I'm almost positive pseudo-F was being calculated back in version
> 15. What is the exact version number (i.e. the output of 'cpptraj
> --version')?
>
> Anyway, I recommend upgrading to at least the AmberTools 18 version of
> cpptraj (or the GitHub version). There have been many improvements and
> enhancements since version 15.
>
> -Dan
>
> On Tue, Jun 26, 2018 at 1:29 PM, Subha Kalyaanamoorthy
> <kalyaana.ualberta.ca> wrote:
> > Hi,
> >
> > I am using version 15.
> >
> > Thanks,
> > Subha
> >
> > On Tue, Jun 26, 2018 at 7:35 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> What version of cpptraj are you using?
> >>
> >> -Dan
> >>
> >> On Fri, Jun 22, 2018 at 2:04 PM, Subha Kalyaanamoorthy
> >> <kalyaana.ualberta.ca> wrote:
> >> > Hi there,
> >> >
> >> > I am trying to cluster a trajectory and write out the info file with
> pSF,
> >> > DBI, SSR/SST information.
> >> >
> >> > I use the below commands,
> >> > ------
> >> > cpptraj -p protein.psf
> >> > trajin protein.dcd 1 9999999 10 \
> >> > cluster out clusters_10 \
> >> > info clusters_10.dat summary summary.dat \
> >> > repout clusters_10 repfmt pdb \
> >> > clusters 10 averagelinkage rms :160-298,545-650,940-1085,
> 1297-1400&.CA
> >> ,C,O,N
> >> > \
> >> > go
> >> > ------
> >> >
> >> > Everything goes well and I get the info file, however, the info file
> only
> >> > writes out DBI (as given below) and not others.
> >> >
> >> > Could somebody suggest me a way to write out these info?
> >> > ______________
> >> >
> >> > #Clustering: 10 clusters 100 frames
> >> > #Cluster 0 has average-distance-to-centroid 0.678705
> >> > #Cluster 1 has average-distance-to-centroid 0.652239
> >> > #Cluster 2 has average-distance-to-centroid 0.619308
> >> > #Cluster 3 has average-distance-to-centroid 0.612557
> >> > #Cluster 4 has average-distance-to-centroid 0.596810
> >> > #Cluster 5 has average-distance-to-centroid 0.588767
> >> > #Cluster 6 has average-distance-to-centroid 0.562917
> >> > #Cluster 7 has average-distance-to-centroid 0.598791
> >> > #Cluster 8 has average-distance-to-centroid 0.552588
> >> > #Cluster 9 has average-distance-to-centroid 0.000001
> >> > #DBI: 1.721831
> >> > #Algorithm: HierAgglo linkage average-linkage nclusters 10 epsilon
> >> > 1.79769e+308
> >> > .....................................XXXXXXXXXXXXXXXXXXXXXXXXXXX...
> >> > .................................
> >> > XXXXXXXXXXXXXXXXXXX.........................................
> >> > ........................................
> >> > ..........................XXXXXXXX.XX...................
> >> > ............................................
> >> > ............................................................
> >> > ....XXXXXXXXX...........................
> >> > ............................................................
> >> > ....................XXXXXXXX............
> >> > ............................................................
> >> > ............................XXXXXXXX....
> >> > ...................XXXXXXX..................................
> >> > ........................................
> >> > ............................................................
> >> > .............XXXXXXX....................
> >> > ............................................................
> >> > ....................................XXXX
> >> > ..................................X.........................
> >> > ........................................
> >> > #Representative frames: 57 8 29 70 87 91 22 77 97 35
> >> > _______________
> >> >
> >> > Thanks,
> >> > Subha
> >> >
> >> > --
> >> > Dr. Subha Kalyaanamoorthy
> >> > Post Doctoral Fellow
> >> > Faculty of Pharmacy and Pharmaceutical Sciences
> >> > University of Alberta
> >> > Edmonton, Canada.
> >> > _______________________________________________
> >> > 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
> >>
> >
> >
> >
> > --
> > Dr. Subha Kalyaanamoorthy
> > Post Doctoral Fellow
> > Faculty of Pharmacy and Pharmaceutical Sciences
> > University of Alberta
> > Edmonton, Canada.
> > _______________________________________________
> > 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
>
--
Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.
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Received on Tue Jun 26 2018 - 12:00:02 PDT
