Re: [AMBER] PCA analysis for side chain atoms and backbone atoms

From: Jorgen Simonsen <>
Date: Wed, 26 Jan 2011 10:52:42 +0100


Just to be quite sure - I think that I remove as much of the rotations
and translations by first aligning the atoms

center :1-100 mass origin

or for backbone .N,CA,C etc? I hope this is correctly understood.

For the side chains, sc, versus backbone.

For sc, I would like to see how much is captured by the first and
second principal component and how big a "space" is expanded by this
side chains. Later, I would like to do quasiharmonic analysis and see
entropy contribution between bb and sc.

On Wed, Jan 26, 2011 at 9:48 AM, Hannes Loeffler
<> wrote:
> On Tue, 25 Jan 2011 20:31:03 +0100
> Jorgen Simonsen <> wrote:
>> Hi all,
>> I would like to make a PCA using ptraj module with ambertools - I am
>> not quite sure how the syntax is though.
>> for the backbone selection I use the following syntax
>> .N,CA,C
>> is there any easier way to select side chains?
>> for an analysis of the side chains will the following syntax make any
>> sense?
>> strip .N,CA,C
>> matrix mwcovar name cc.matrix out cc.matrix
>> analyze matrix cc.matrix out new.matrix
> Just wondering.  What exactly do you expect to see from a side chain
> PCA?  The side chains will mostly follow the backbone movements but
> also have some independent movement of their own.  The side chain modes
> will be just somewhat weaker than their corresponding main chain
> modes.  Directions may also be slightly different.
> Don't forget to also remove rotations and translations for the
> selected atoms first.
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