AMBER Archive (2003)

Subject: Re: AMBER: Protein Rotation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Nov 11 2003 - 10:35:08 CST

> Use FIT with your RMS statement.

And be aware that in periodic simulations (especially longer
ones and ones with small box clearance) solute residues can be
translated across the box, leading to an artifactually bad
RMS fit/measurement. (And this will always be the case with
solvent.) When residues whose rms is being measured are
translated with respect to one another, the translation must
first be removed, which is a bit of an art. Carnal has the
IMAGE function for this; Ptraj has had more work put into this
functionality, see the manual for details.

Bill Ross

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