Dear Harald,
I can send you a Perl module that can parse ptraj eigenvector files.
You could then calculate a dot product between all vectors of the two
different complexes, provided that the structures have been aligned to
a common reference prior to calculating the modes.
Let me know if this is of interest to you.
Best regards
Holger
Quoting Harald Lanig <Harald.Lanig.chemie.uni-erlangen.de>:
> 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 chemie.uni-erlangen.de
> Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig
> ------------------------------------------------------------------------
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 18 2007 - 06:07:05 PST
