Although I haven't had a chance to use PCA in AMBER yet, I have used Bio3D
to make a movie from PCA motion that can be viewed in VMD.
If you want to qualify domain motion, you could try using Local Feature
Analysis. I remember reading an interesting paper on applying the
technique to biomolecules by Zhang and Wriggers in Proteins, 2006.
> Dear AMBER Users,
>
> I am trying to study domain motions in my protein using PCA analysis of
> the
> ptraj module. I have successfully performed PCA and have got the
> projection
> files.
>
> The next problem is to visualize the motions and generate porcupine plots.
> For
> this, I installed ied-2.02 as a plugin in VMD 1.8.6. The plugin seems to
> work
> fine with gromacs examples but fails to work with AMBER format files. I
> checked
> online and it says that ied can only use formats generated using ptraj8.
> Is this
> true?? Also i am not able to draw the arrows using this plugin , which
> seems to
> be a bug with vmd 1.8.6.
>
> I can use PCASuite, however my CRD files are in the .gz format and
> PCASuite is
> not able to read the gunzipped files. Also, I have a set of 20 CRD files
> and I
> want PCASuite to read all the CRD files one after another, how can this be
> done???? Is there a way of scripting PCASuite, wherein one can use trajin
> command and PCAsuite in combination ??
>
> Finally, can some one take me through the process of generating poocupine
> plots
> from the PCA analysis done using ptraj of AMBER 9. Also, is there a way of
> quantifying domain motions. Is it ok if i calculate the angles between
> two set
> of residues from the centre of the domains ???
>
> Thanks,
> Soma
>
>
>
>
>
>
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Received on Fri Sep 20 2013 - 09:30:03 PDT
