AMBER: Comparison of normal modes with ptraj?

From: Harald Lanig <>
Date: Wed, 14 Feb 2007 11:10:19 +0100

Dear amber community,

I am interested in how different ligands affect the normal modes of
always the same protein. Therefore, I performed an ptraj analysis of the
trajectories always following the scheme:

rms to reference
matrix mwcovar
analyze matrix
projection modes

to get the mass-weighted modes and projections for visualization eg with
vmd. All this works fine. The remaining question is:

How can I compare the modes from different simulations? Is there a
possibility to calculate an "inner product" between all modes to get a
"similarity index array"? I need to quantify their similarities to get
information like "mode 2 in simulation 1 is most similar to mode 3 in
simluation 2".

Any help or hint is highly appreciated!

Kind regards,
-Harald Lanig

  Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
  Phone +49(0)9131-85 26525   email: lanig AT
  Fax   +49(0)9131-85 26565
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Received on Sun Feb 18 2007 - 06:07:03 PST
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