AMBER: Coordinate Superimposition in PTRAJ

From: Vineet Pande <>
Date: Sun, 16 Jan 2005 11:42:09 +0000

Dear Scientists:
I want to superimpose a number of 'different' complexes of the 'same
protein' with different ligands obtained after a PME/PBC MD protocol, and
refinement. So, I want to use, say a given complex (having its coordinates +
topology file, with box of waters) as a TEMPLATE and superimpose ONTO IT
around 25 complexes of the same protein (strip off waters/counterions),
based on C-alpha/ heavy atoms >> and get "modified-coordinates" of all the
complexes. Does anyone have a PTRAJ script for this purpose.

Of course, a superimposition might be done in a graphics program like
Insight, but the hydrogen names of Insight outputs don't match with Amber
style.....Does any one have solution to this problem, otherwise.

With thanks in advance,

"The future belongs to those who believe in the beauty of their dreams"
-Eleanor Roosevelt

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Received on Sun Jan 16 2005 - 12:53:00 PST
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