[AMBER] pre-processing of trajectories

From: <moitrayee.mbu.iisc.ernet.in>
Date: Wed, 23 Jun 2010 19:32:08 +0530 (IST)

Dear Amber Users,

I am doing PCA analysis with ptraj using Ambertools 1.4.

I am using the following script.


/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


Will this script take care of any periodic imaging artefact in the system befor
doing PCA?
Please help me out with this issue.

Thanks a lot in advance.

Sincere Regards,

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Received on Wed Jun 23 2010 - 07:30:03 PDT
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