AMBER Archive (2005)

Subject: AMBER: Antechamber help needed

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Feb 17 2005 - 11:24:34 CST

I'm trying to create a modified guanine residue using Antechamber.
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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