AMBER Archive (2009)

Subject: [AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift

From: Andrew Voronkov (
Date: Sun Aug 23 2009 - 06:55:01 CDT

Dear Amber users,
I want to evaluate the drift of peptide ligand from the binding site on the protein surface (the movements in the binding site and evaluation of the parts of peptide with the highest stability of position against the protein).

Question 1:
Are there any significant differences between ptraj and carnal for this purpose?

Question 2
If I want to evaluate RMSD of center of mass drift - is it the same as mass weighted RMSD like this:

trajin s4_full.mdcrd
rms mass first out s4_ca-123-140.rms :123-140_at_CA time 10

Question 3
In all these procedures only RMSD of coordinates in trajectory against initial state is calculated right? So I'll get not the drift of peptide against the binding site, but the drift of peptide from its initial position? (which doesn't account the possible changes of the binding site structure and drift of protein?) So I need to evaluate RMSD of some peptide atoms against ptrotein binding site atoms?

Sincerely yours,

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