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?
Please help me out with this issue.
Thanks a lot in advance.
Sincere Regards,
Moitrayee
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Received on Wed Jun 23 2010 - 07:30:03 PDT
