Dear All,
Thank you for very much for the suggestions. It is of great help.
Regards
Sowmya
________________________________________
From: Elvis Martis [elvis.martis.bcp.edu.in]
Sent: Monday, September 25, 2017 3:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] cluster analysis using cpptraj
Hi,
Just to add to BIll's and Thomas' answer on this.
If you want to use DBSCAN method there is small precalculation you can run to identify what might be suitable parameters for your system (however these are just hints, you may still need to tweak somethings)
Here I am paraphrasing from the AMBER17 manual (pg 656)
Hints for setting DBSCAN parameters with ’kdist’
It is not always obvious what parameters to set for DBSCAN. You can get a rough idea of what to set ’mindist’
and ’epsilon’ to by generating a so-called "K-dist" plot with the ’kidst <k>’ option. The K-dist plot shows for
each point (X axis) the Kth farthest distance (Y axis), sorted by decreasing distance. You supply the same
distance metric and sieve parameters you want to use for the actual clustering, but nothing else. For example:
--------------------------
cluster C0 dbscan kdist 4 rms :1-4.CA (replace suitable atom masks for your case) sieve 10 loadpairdist pairdist CpptrajPairDist
--------------------------
Best Regards
Elvis Martis
Mumbai, INDIA.
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Received on Mon Sep 25 2017 - 07:30:02 PDT
