AMBER Archive (2009)

Subject: [AMBER] nmode output

From: Vahdati N. (nadiav_at_soton.ac.uk)
Date: Wed Aug 05 2009 - 17:26:11 CDT

Dear amber users,

Is there a way of analysing the degree of overlap between eigenvector outputs from Nmode or (pca for that matter), in ptraj, similar to that with g_anaeig in Gromacs.
 For instance to establish the overlap between 2 eigenvectors from two different NMA runs.

Has anyone developed codes that would have this capability in application to amber format eigenvector files.

Additionally, I would like to establish which modes contribute to movement in particular sections of my protein, without having to visualise each one. Are there any tools available for application to amber NMA outputs?

Thank you in advance for any comments,

Nadia

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