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
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Received on Tue Jun 26 2018 - 11:00:03 PDT
