AMBER Archive (2005)

Subject: AMBER: writing MASKs

From: Sagar D Khare (khare_at_email.unc.edu)
Date: Fri Apr 22 2005 - 09:58:24 CDT


Hi,

I am trying to analyze a protein trajectory, and want to calculate the
following: (a) residue-wise side-chain RMSDs of all or a subset of
residues (b) RMSD of residues within say a 4 A sphere of a particular
side-chain. I did not find in the manual a description of the Amber API to
help write these masks (for the backbone there is "@N, C, CA", but how do
I select a specific set of reisues?). Any pointers?

Thanks in advance,

Sagar

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