AMBER Archive (2002)

Subject: a question about force field in AMBER

From: jzhou (jzhou_at_sunkay.cs.ualberta.ca)
Date: Sat Dec 14 2002 - 19:55:15 CST

Hi,

I am a student in Department of Computer Science in University of Alberta. I
am doing a project on energy minimization and am using your force field
function to calculate the potential energy of the proteins from the Protein
Data Bank.

My question is, given the coordinates of two atoms, could I decide whether
they are bond or non-bond simply from their distance? Is their any empirical
value to distinguish bond and non-bond pairs?

Thanks and Merry Christmas.

Jun Zhou