Re: [AMBER] Dynamic cross correlation matrices in AMBER20

From: Matias Machado <>
Date: Wed, 17 Nov 2021 17:53:51 -0300 (UYT)

Dear Bebarati,

I didn't check the cpptraj manual, but you may try any of these two software:

Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

Hope this helps...

Best regards,


----- Mensaje original -----
De: "Debarati DasGupta" <>
Para: "" <>
Enviados: Miércoles, 17 de Noviembre 2021 13:50:00
Asunto: [AMBER] Dynamic cross correlation matrices in AMBER20

“Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions”…
In these lines a reviewer asked me to check if I can calculate the cross correlation matrices in my CoV2 main protease (residue NXN maps) and check if there is any allosteric motion…
I am not too sure but I would want to analyze my cosolvents simulation trajectories and plot these cross correlations…
Is there a way Cpptraj can make this task doable?
I am using AMBER20

Thanks all in advance.

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