AMBER Archive (2006)

Subject: Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction

From: Mingfeng Yang (
Date: Mon Aug 14 2006 - 14:06:56 CDT

Thank you, Dr. Cheatham. Because the structure and stability of a turn can
be affected by various of factors, I want to keep the side-effect as minimum
as possible. TI seems a very good choice here. Thanks!

Best regards,

On 8/14/06, Thomas Cheatham <> wrote:
> > I know that a specific residue (Ser) can form multiple hydrogen bonds
> with
> > other residues in the same protein, which should help to form and
> stabilize
> > a turn structure. Now I want to investigate the importance this hydrogen
> > bond. The charge of oxygen atom in the hydroxyl group of Ser is -0.6546,
> and
> > 0.4275 of hydrogen thereof. I plan to increase the charge of oxygen atom
> > gradually to zero, and decrease the charge of hydrogen atom with the
> same
> > quantity at the same time, and observe the hydrogen bond network of this
> Ser
> > residue. This modification will be applied to the interaction between
> Ser
> > and all other residues, but when the intra-residue interactions are
> > evaluated, the charges remain the same as what amber force field gives.
> Does
> > my research design make sense?
> I am unclear as to why you want the "intra"- residue interactions to be
> the same (noting that the 1-2, and 1-3 exclusions prevent the O--H from
> interaction). The change in charge may well alter the torsional profiles
> of the hydroxyl side chain but will likely have little effect on the
> backbone.
> There are a couple of ways I might try to see the effect of the serine
> (without any code modifications).
> (1) Force the charge change via the thermodynamic integration facility to
> perturb the charge in stages. This will allow you to "see" what effect
> the change has on the conformational equilibria (noting that a change in
> this equilibria will mean that a lot of sampling is required to have the
> resulting free energies make any sense). This change in charge is easy
> to watch, but how do you correlate this back to experiment?
> (2) Instead, perturb the SER to ALA (both in the "unfolded" and hairpin
> geometry so that you have a complete cycle). This is experimentally
> accessible.
> \-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> -/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
> /-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
> \-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
> -/-
> /-\ (801) 587-9652; FAX: (801) 585-9119
> \-/ BPRP295A
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