AMBER Archive (2009)

Subject: [AMBER] reg . run TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Feb 10 2009 - 11:36:28 CST

Dear Amber,
        
        
        
        
        
        
        

I would like to do Targeted Molecular
Dynamics for DNA .
I am having the crystal structure of
two different DNA structures

from the same sequence among them one
is a junction

the all atom RMSD between the two is
14.54.

among this two i kept one as a
referance coordinate.is it possible to do TMD with such a huge RMSD difference ,
I saw the test case given in the package
i could not under stand the minimization procedure
can any one suggest me how minimization to be carried out .thanks in advance
balajiUOM

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