AMBER Archive (2008)

Subject: Re: AMBER: Hydrogen bond energies in explicit solvent.

From: Carlos Simmerling (
Date: Mon Sep 15 2008 - 10:01:41 CDT

please note that the amber developers recommend that you do NOT use
ff99. many studies have shown that this is not a good model. please
use ff99SB or ff03 (ff99SB is newest).

what do you mean by the "HB field"? there are no explicit hydrogen
bonding terms needed, it will be handled by the electrostatics. the
same is true for ff99, ff03 and ff99SB.

On Mon, Sep 15, 2008 at 10:56 AM, Waqas Nasir <> wrote:
> Hi,
> 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,
> Thanks,
> Waqas.
> PS: I am using amber version 8.0 with ff99 and glycam06 forcefields.

Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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