AMBER Archive (2006)

Subject: AMBER: ACTIVE SITE

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Mon Jan 16 2006 - 08:06:52 CST

Hi all,

i guess this is a really silly question but here goes- i am trying to run
pca analysis exclusively on the active site of a protein after dynamics.
thus in ptraj i need to identify the residues that make up the active site.
I was wondering do I quote specific aas like ALA 561 from the pdb file, or
do i need to quote the individual atoms that make it up? or is there some
other way of doing it altogether- in the sense that when i code for backbone
atoms, i do not use a pdb reference file.

THANKS

claire

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