AMBER Archive (2004)

Subject: AMBER: Ideal bonds and angles

From: Nhat-hang Duong (nhduong_at_rci.rutgers.edu)
Date: Tue Dec 21 2004 - 11:49:38 CST

Hi all,

At the end of a minimization run, the output gives a summary where it is
stated that:

RMS deviation from ideal bonds: xyz
RMS deviation from ideal angles: abc

I assume that the RMS is done with the "ideal" configuration as a
reference. What is the "ideal" configuration in this case? Is it
possible to set this to any configuration I want?

Thanks,
--Hang
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