AMBER Archive (2002)

Subject: limit of RMSD value

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Tue Nov 19 2002 - 07:57:40 CST

Dear Amber users,

I'd like to know is it any maximum limit for RMSD value? Is it any criteria for RMSD value to say our structure is not distorted from starting structure? I agree with people who say above 2 Angstrom is very distorted structure, but why 2 Angstrom? Why not 1.5 or 0.5 Angstrom?

I'm using ptraj to plot 2dRMS graph. As far as I know, ptraj uses maximum value as 2dRMS limit value. I have tried to use smaller limit and I got different results. That's the matter of limit value. Can anybody give me any literature which discuss about RMSD limit value?

Regards,
Bimo 

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