AMBER Archive (2008)
Subject: AMBER: Hydrogen bond energies in explicit solvent.
From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Hope every thing is working fine at your side.
Just wanted to ask about the HB field for the mdrun with explicit solvent. I have this field zero for the explicit solvent with solventcap option used. Is this because of the ff99 force field or is it due to something else? Is there a way to calculate the energy for HB? Moreover, will this not be the case with ff03 forcefield.
Appreciate your comments,
PS: I am using amber version 8.0 with ff99 and glycam06 forcefields.