AMBER Archive (2005)

Subject: AMBER: Mainchain example needed

From: Kara Wald (kdigiorgio_at_sbcglobal.net)
Date: Mon Feb 14 2005 - 15:43:06 CST

I'm trying to create a modified guanine residue. I've been following
the " Generate amino-acid-like residue topology file ... " tutorial.
In it, I need to create a mainchain file to generate my prepin file.
I've been able to understand all the elements needed except which atoms
to include under MAINCHAIN . (Do I only include the sugar in the
mainchain? Do I include the sugar and the base? Do I include the sugar,
base and the compound that's covalently bound to the base? Do all atoms
get included? Do hydrogens get omitted? etc) Does anyone have a
mainchain definition file for a DNA residue that I could look at? I
think an example would help me understand a lot better.

Thank you,

Kara Di Giorgio
University of the Pacific

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