VMD-L Mailing List

From: Ignacio Fernández Galván (jellby_at_yahoo.com)
Date: Tue Oct 26 2010 - 11:47:18 CDT

Hello,

I was searching for an algorithm to align (superpose) two molecules, and found
these related references:

Acta Chrystallogr. Sect. A 61 (2005) 478 [doi: 10.1107/S0108767305015266]
J. Comput. Chem. 31 (2010) 1561 [doi: 10.1002/jcc.21439]
More info: http://theobald.brandeis.edu/QCP/

This is apparently a fast and efficient method to obtain the optimal rotation
matrix. Being so new (particularly the second), I don't think VMD has this
method implemented, and I wonder if it could benefit from it, especially when a
great number of structures have to be aligned (as with the RMSDTT plugin).