AMBER: ptraj

From: Marcela Madrid <>
Date: Fri, 09 Jun 2006 17:19:54 -0400


I am trying to calculate PCA from a correl. matrix, and it does not
work. (This is ptraj from amber8). However, the same script works if I
use covariance matrix instead of correl. Is there a reason for this?
I am using the trajectory that comes with the ptraj test.
Here is the input file:

trajin 1rrb_vac.mdcrd
matrix name matrix.correlmemory correl out matrix.correl
analyze matrix matrix.correlmemory out pcacorrel vec 2

This calculates the correl. matrix but when trying to analyze gives the
PTRAJ: Successfully read in 10 sets and processed 10 sets.
        Dumping accumulated results (if any)

PTRAJ MATRIX: Dumping matrix values

PTRAJ: Analyzing accumulated data
./Run.example: 569391 Floating exception

The same script, replacing correl by covar, works.

Thanks, Marcela

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Received on Sun Jun 11 2006 - 06:07:18 PDT
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