[AMBER] Error while clustering on CPPTRAJ

From: <dnlfr1994.gmail.com>
Date: Thu, 14 Jan 2021 14:03:45 +0100



I’ve been doing some clustering tests on several trajectory files, using the
dbscan algorithm. As mentioned in the manual, I am running the kdist option
to choose appropriate epsilon and k values. In order to speed up the process
I have used the savepairdist and loadpairdist commands. However, I am
getting the following error with some trajectories --> Error: Number of
columns in file changes at line 100.

I suspect the problem appears when loading the pairdist matrix file, since
the number of times this error shows up matches with the number of times
that my scripts loads the matrixfile.

However, the final kdist plots (see figure below) seem to be OK.


Does anyone know why this error is happening?


By the way, the shape of the curves does not change much after kdist=4 (as
explained in the user’s guide), but the height still varies remarkably even
with kdist=10. I am not sure if the epsilon and k values of any of these
tests can be used for the final clustering or more tests would be required.


Any help is really appreciated.


Daniel Fernández

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Received on Thu Jan 14 2021 - 05:30:02 PST
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