AMBER Archive (2004)

Subject: Re: AMBER: Sander & fix atoms

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jun 03 2004 - 16:06:04 CDT

> 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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