[Chimera-users] Circular DNA minimization

Damien Larivière damien.lariviere at fourmentinguilbert.org
Sat Dec 29 07:40:00 PST 2012


Dear all,

I'm currently minimizing a circular DNA molecule, relatively large (~11 
000 atoms). I use "Minimizing structure" in Structure editing.

The first phase, the Steepest Descent Steps, works fine.

However, the second one, the Conjugate Gradient Steps, looks like 
blocked with the message "dock prep finished" at the bottom of the screen.

If I remove one base pair so that the molecule is no more cyclized, then 
the second minimization stage starts as expected.

I'm not versed in the art of minimization. Do you know the reason of 
this behavior?

Thanks for your help,

Damien

ps: I'm working on Windows 7 with a core i5


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