AMBER: Antechamber help needed

From: Kara Di Giorgio <>
Date: Thu, 17 Feb 2005 09:24:34 -0800

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Feb 17 2005 - 17:53:00 PST
Custom Search