Re: AMBER: Not getting proper structure after minimization

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From: Carlos Simmerling <carlos.csb.sunysb.edu>
Date: Wed, 25 Oct 2006 09:45:38 -0400

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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----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu Received on Sun Oct 29 2006 - 06:07:06 PST