AMBER Archive (2006)

Subject: Re: AMBER: Not getting proper structure after minimization

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Oct 25 2006 - 08:45:38 CDT

note that we recently published a detailed comparison of
Amber force fields that should be very useful to people
starting out on a protein simulation project.

Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling, C., “Comparison of multiple Amber force fields and development of improved protein backbone parameters”, Proteins: Structure, Function and Genetics, 3:712-725 (2006).


Elijah Gregory wrote:
As far as parameter sets.... you should know that most forcefields out
there overemphasize alpha-helix structure....  it's trickier to
simulate alpha/beta structures. Look in the literature for *anything*
done with MD and your protein (or related homologues) for more  hints
and tricks.  MD is not easy, but nothing ever is =P

~Elijah
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