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