Hi
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
<Hannes.Loeffler.stfc.ac.uk> wrote:
> On Tue, 25 Jan 2011 20:31:03 +0100
> Jorgen Simonsen <jorgen589.gmail.com> 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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Received on Wed Jan 26 2011 - 02:00:02 PST
