AMBER Archive (2008)

Subject: Re: AMBER: Protonated Phosphate Problem

From: Thomas Steinbrecher (
Date: Tue Jul 01 2008 - 12:41:55 CDT

Hi Michal,

AFAIK, there is no new or good solution to the protonated phosphate
problem, the ad-hoc solution is to put a small vdw radius on them (e.g. by
changing the H-type to HS) but I dont know if anybody ever stress-tested
that. I am working on a reparametrisation of phosphates at the moment with
Dr. Case, but that might take a while to finish up. Be aware that free
energies that you might want to compute with your phosphorylated systems
will not come out very accurate right now, no matter what you do to the



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Tue, 1 Jul 2008, Kliman, Michal wrote:

> Dear Amber Community,
> I browsed the old attempts at correcting the behavior of the protonated
> phosphate but I am wondering whether there are any new
> suggestions/solutions in Amber 10, Amber 9.
> I am using Amber to do conformational sampling of individual lipid
> molecules and short DNA single strands (trimers) in vacuum.
> In vacuum, at high temperature needed for proper conformational sampling,
> probably the overlap between the proton an a near oxygen causes the 1-4
> electrostatic term to heat up the molecule to extreme temperatures and the
> simulation / sampling crashes.
> Any NEW ideas on how to correct this problem with the protonated
> phosphate? I need a physical proton on the phosphate because it plays an
> important role in the coordination of the lipid / DNA molecules in vacuum
> and therefore is a key element of the fragmentation processes observed by
> mass spectrometry.
> Thanks.
> Michal
> grad student
> Vanderbilt University
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