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
[
https://doi.org/10.1021/acs.jcim.1c00742]
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics
https://doi.org/10.1016/j.csbj.2021.08.043
Hope this helps...
Best regards,
Matías
----- Mensaje original -----
De: "Debarati DasGupta" <debarati_dasgupta.hotmail.com>
Para: "AMBER.ambermd.org" <amber.ambermd.org>
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.
Debarati
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Received on Wed Nov 17 2021 - 13:00:02 PST
