AMBER Archive (2009)

Subject: [AMBER] matrixinfoStack

From: Naser Alijabbari (
Date: Tue Nov 10 2009 - 08:45:12 CST

We wanted to try a new procedure where an averaged matrix was used. For
example we wanted: ave.matrix=(*matrix1+*matrix2+*matrix3+*matrix4)/4.
However I don't know how to feed the averaged matrix, which was averaged
using Matlab, to Amber.

Previously the following commands were used for finding eigenvalue and
eigenvectors from trajectories:

trajin bbprotein_noWat_rms.mdcrd 1 12000

matrix mwcovar name protein.matrix out protein.matrix

analyze matrix protein.matrix out protein.mode vecs 400

In Amber the trajectories were read, the matrix was calculated and placed on
the computer stack, and the matrix was diagonalized to find the
eigenfrequencies (x,y,z values) and eigenvectors (amplitude). I don't know
how an averaged matrix can be placed onto the stack for the calculations to
(the following error is returned: ptraj(), analyzeMatrix: cannot find a
match in the
                                            matrixInfoStack for name
(ave.matrix), returning.)
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