AMBER Archive (2000)

Subject: parametrization

From: Cristina Dezi (cristina.dezi_at_pharma.anbi.ethz.ch)
Date: Thu Mar 30 2000 - 02:06:56 CST

I'm trying to calculate charge (using RESP) for cation Mg which
coordinates the three phosphatus of ATP, two residues, one water
molecule. For ATP, I started with a truncated system (just a methyl
triphosphate) and now I'm considering the whole ATP using the charge
previously calculated for the phosphate group as constraint in resp.in.
But I obtain abnormal charges on the sugar moiety (ex: +4 on C3'). As I
read in the paper about the development of AMBER force field that the
authors didn't use the whole ATP, I asked myself if there is a problem
with the whole molecule.

Thank everyone in advance

Cristina Dezi