AMBER Archive (2009)

Subject: Re: [AMBER] the different RMSD?

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Nov 13 2009 - 21:40:56 CST

> I use ptraj to analyze my result, the rmsd goes up to more than
> 6,but when I load the same structure to the Pymol using the identical
> reference structure, the rmsd was only about 2, I am very confused about
> this problem.

We need more details; what was your ptraj script and how did you specify
the reference structure. Were both the ptraj and Pymol RMS fits by mass?

-- tec3

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