AMBER Archive (2004)

Subject: Re: AMBER: Amber & mutation

From: Tim Meyer (tim_at_mmb.pcb.ub.es)
Date: Thu Jun 10 2004 - 00:14:11 CDT


> imin=1, ncyc=250, maxcyc=500, ntb=0,
> they do, energy minimization supposes to fix the bad contacts, and result
> to changed helix structure? Or the current structure modeling methods

in 500 steps minimization you won't find any structural changes. run a
md, a nanosecond or so, and see what happens. you should also run a
control md of your 'wild type' helix

tim

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