Can you provide me (either in reply to this or off list) your entire
cpptraj output and the contents of dvdfile?
This could happen with very sparse density I think, although its
difficult to say without exactly replicating. You could potentially
try the 'gauss' keyword for Gaussian density instead of discrete
density.
-Dan
On Mon, Jan 13, 2020 at 8:10 PM Yinglong Miao <yinglong.miao.gmail.com> wrote:
>
> Hi Dan,
>
> It’s the latest version as in AMBER git repository.
>
> Thanks,
> Yinglong
>
>
> > On Jan 13, 2020, at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > What version of cpptraj are you using?
> >
> > -Dan
> >
> > On Mon, Jan 13, 2020 at 6:51 PM <yinglong.miao.gmail.com> wrote:
> >>
> >> Hello,
> >>
> >> I tried to use the dpeaks algorithm for clustering with the following
> >> command:
> >> cluster C0 dpeaks epsilon 4 dvdfile dvdfile choosepoints auto runavg
> >> runavg.dat deltafile delta.dat sieve 200
> >>
> >> But keep getting the following output with error:
> >> ...
> >> Finding closest neighbor point with higher density for each point.
> >> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
> >> Internal Error: In Cluster_DPeaks::AssignClusterNum nearest neighbor is -1.
> >> Segmentation fault (core dumped)
> >>
> >> I will appreciate any suggestions that would fix this ...
> >>
> >> Thanks,
> >> Yinglong
> >>
> >> Yinglong Miao, Ph.D.
> >> Assistant Professor
> >> Center for Computational Biology and
> >> Department of Molecular Biosciences
> >> University of Kansas
> >> http://miao.compbio.ku.edu
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Jan 14 2020 - 08:00:02 PST
