AMBER Archive (2004)

Subject: Re: AMBER: Sander & fix atoms

From: bybaker_at_itsa.ucsf.edu
Date: Thu Jun 03 2004 - 17:32:53 CDT


('binary' encoding is not supported, stored as-is) On Thu, 3 Jun 2004 14:06:04 -0700 (PDT) Bill Ross wrote:

> > The minimization will be done in three steps: (1)
> > fixed heavy atoms (all but hydrogen), (2) fixed backbone atoms with
> > tethered atoms, (3) tethered backbone atoms.
>
> This is probably a waste of time unless you have a very
> rough hand-built or -modified structure. Minimization does
> not do very much to change a normal structure as a rule -
> I'd first try a simple min and compare the superimposed
> structures.
>
> Bill
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