AMBER Archive (2008)

Subject: Re: AMBER: hold atoms fixed

From: Gustavo Seabra (
Date: Mon Jun 30 2008 - 09:10:53 CDT

> But after minimization, when I visualised the correspondin pdb i find that
> all atoms in part2 has moved as well.

How much do the atom move? Is it really a lot? Notice that you are not
freezing the atoms, but only restraining them, which only applies a
penalty to moving them: depending on the initial structure, they might
still move. If you really want to freeze those atoms, *maybe* you
could use ibelly, but I'm not sure it works with minimization.

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