Re: [AMBER] cpptraj error

From: Daniel Roe <>
Date: Mon, 19 Nov 2018 09:00:25 -0500


Your issue is here:

On Mon, Nov 19, 2018 at 7:59 AM Rajbinder Kaur Virk
<> wrote:
> No clusters found.

This isn't a cpptraj error per se. Based on the parameters you gave
the 'cluster' command, no clusters were found. You'll need to try to
adjust the parameters you're giving the DBSCAN algorithm, or try
another algorithm. Clustering is much more of an art form than a
science, so plan on a fair amount of trial and error here. It's good
that you're starting off with a relatively small trajectory; this will
allow you to become familiar with the results without waiting around
too much. I highly recommend reading the entire 'cluster' command
entry in the Amber 18 manual if you haven't already (section 29.11.4,
starting on page 694), and in particular the 'Hints for setting DBSCAN
parameters' subsection if you want to continue using DBSCAN. I also
recommend reading this excellent paper on clustering MD trajectories
from Shao, Cheatham et al.:

Some general clustering tips:

1) In my experience I've obtained better results with 'sieve <#>
random' as opposed to plain 'sieve <#>'.
2) If you're not going to change your distance metric (including
sieve) you way want to use 'savepairdist'/'loadpairdist' to avoid
recalculating the pairwise distances every time. This is useful e.g.
when doing hierarchical aggolmerative with varying epsilon, etc.
3) The OpenMP version of cpptraj (cpptraj.OMP) can accelerate the
pairwise distance calculation, but don't use more threads than you
have physical cores.

Also, there is a very basic clustering tutorial you may find useful

Hope this helps,


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Received on Mon Nov 19 2018 - 06:30:04 PST
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