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

From: Debarati DasGupta <>
Date: Mon, 6 May 2019 20:27:46 +0000

Hi Daniel,

Could you send me a sample input file (which can do hierarchical agglomerative based clustering)

I am finding it hard to implement it using the manual of Amber18

Thank you in advance!


From: Daniel Roe<>
Sent: Tuesday, April 30, 2019 9:43 AM
To: AMBER Mailing List<>
Subject: Re: [AMBER] Any help on how to implement it in cpptraj?


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 ĒŠA 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list

AMBER mailing list
Received on Mon May 06 2019 - 13:30:02 PDT
Custom Search