AMBER Archive (2008)

Subject: AMBER: local coordinate system question

From: caoch (
Date: Wed Jun 25 2008 - 04:33:15 CDT

Hello all:


   I want to calculate some ligand polarlizabilities using Amber
polarlizable forcefileld with Thole screening model.

To compare with experimental results, a new local coordinate system should
be defined and the target ligand should be changed from global coordinate to
the local one. (Such as Gaussian package do standard rotation by using
"Symmetry" keyword).


  Does someone know the algorithm of defining the residue (ligand) local
coordinate system and some open tools for rotating coordinate system?


  Best regards

JST-CREST Researcher
Fundamental Technology Laboratory
Research and Development Division
Mitsubishi Chemical Group Science and Technology Research Center, INC.
1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
TEL +81-45-963-3264


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