[AMBER] PCA analysis and porcupine plots

From: Soma Ghosh <soma.mbu.iisc.ernet.in>
Date: Fri, 20 Sep 2013 11:28:54 +0530 (IST)

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

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 ???


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Received on Thu Sep 19 2013 - 23:00:03 PDT
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