AMBER Archive (2003)

Subject: how to validate ff parameters obtained from antechamber

From: Jiyoung Heo (jyheo_at_wag.caltech.edu)
Date: Thu Feb 27 2003 - 23:27:54 CST

Dear amber users,

I generated the force field parameters for non-natural DNA bases using
antechamber. They have just some modification, so the common FF
parameters were taken from natural DNA base parameters and non-available
ones in parm98.dat were from the antechamber output.
I am wondering how you validate the force field parameters obtained by
antechamber.
Do you usually calculate base pairing energy and compare the QM result?
What is the best and reliable way?

-Jiyoung