On Wed, 23 Jun 2010 19:32:08 +0530 (IST)
moitrayee.mbu.iisc.ernet.in wrote:
> Dear Amber Users,
>
> I am doing PCA analysis with ptraj using Ambertools 1.4.
>
> I am using the following script.
>
> #!/bin/sh
>
> /soft/amber11/exe/ptraj 2zni.prm.top << EOF
>
> trajin 2zni.0030_0040.crd
> trajin 2zni.0040_0050.crd
>
> rms first out rms .CA
> matrix covar name 2zni_covar .CA out 2zni_covar.dat
> analyze matrix 2zni_covar name 2zni-pca out 2zni_pcavec.dat vecs 100
>
> center .CA
> image origin center
> strip :WAT
>
> go
>
> Will this script take care of any periodic imaging artefact in the
> system befor doing PCA?
If you want that to happen you will also have to invoke the center and
image commands BEFORE doing PCA, i.e. before the RMS fit.
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Received on Wed Jun 23 2010 - 08:00:04 PDT
