Re: [AMBER] Any help on how to implement it in cpptraj?

From: Daniel Roe <>
Date: Tue, 30 Apr 2019 09:43:21 -0400


The 'leader' algorithm is not implemented in cpptraj. From my limited
knowledge of it, probably hierarchical agglomerative is the closest
one in cpptraj (although you may want to try others, like k-means).

The distance-RMSD metric is available in cpptraj, although in practice
I have not found it much different from basic RMSD with fitting.

Hope this helps,


On Fri, Apr 26, 2019 at 12:25 PM Debarati DasGupta
<> wrote:
> I am trying to do ---->Analysis of MD simulations and clustering procedure.
> I need to implement the leader algorithm for clustering according to the distance root mean square between two MD snapshots a and b,
> which was calculated using the intermolecular distances dij between pairs of non-hydrogen atoms in acetonitrile and eight residues in the ABL-KINASE active site. A DRMS threshold of 1 ˚A is needed for clustering by the leader algorithm. The DRMS calculation does not require structural overlap."
> Any input files how to implement it in cpptraj AMBER18?
> I am trying to reproduce the methodology of " Small Molecule Binding to Proteins: Affinity and Binding/Unbinding Dynamics from Atomistic Simulations Danzhi Huang* and Amedeo Caflisch*"
> Debarati
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Received on Tue Apr 30 2019 - 07:00:02 PDT
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