AMBER Archive (2008)

Subject: AMBER: Protonated Phosphate Problem

From: Kliman, Michal (
Date: Tue Jul 01 2008 - 12:20:14 CDT

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.


grad student
Vanderbilt University

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