AMBER Archive (2005)

Subject: RE: AMBER: writing MASKs

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Fri Apr 22 2005 - 10:45:43 CDT

Some examples..

:1_at_C :2_at_N :2_at_CA :2_at_C will select from residues 1 or 2 the @follwed atom
type
:1-354_at_CA will select all CA types from residues 1 to 354 only

Cheers
Vineet

>
>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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