ptraj --- 2drms

From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Mon Feb 18 2008 - 09:52:46 CST

You guys maybe the wrong people to ask this question, but does anyone know how the 2drms command in ptraj works? Specifically what the atom-mask relates to. What I want to do is calculate the 2drmsd of a part of a residue in a protein, by aligning the rest of the residue (which should be pretty immobile comparitively). Does the mask refer to the atoms used for the alignment or for the atoms used for the calculation of the rmsd?

Mr Philip Peartree MSc AMRSC
Computational Enzymology
University of Manchester

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