Re: [AMBER] The parameters for the fully protonated phosphate group

From: David A Case <>
Date: Mon, 21 Nov 2016 09:08:04 -0500

On Mon, Nov 21, 2016, jinfeng liu wrote:
> Recently I am doing molecular dynamics simulation for a molecule
> which contains a fully protonated phosphate group. The Antechamber is used
> to generate the parameters for the molecule.The atomic charges are fitted
> using RESP method in HF/6-31G* level. However, when I used these parameters
> to minimize the molecule, the hydroxylic hydrogen atom always had a bad
> contact with its neighboring oxygen atom which double bonded to the
> phosphorus atom. And this lead to the failure of MD simulation. I tried the
> BCC charges, but this problem was still existed. The initial structure of
> the molecule is 100% OK. So, can anyone tell me how to solve this problem ?

This is a general problem with models of protonated phosphates that have zero
vdW radii on the hydrogens. You may be able to solve the problem by changing
some angle parameters: see comments about "preventing simulation
instabilities" in $AMBERHOME/dat/leap/parm/frcmod.phosaa10, and in the
corresponding paper:

# T. Steinbrecher, J. Latzer, and D.A. Case.
# Revised AMBER parameters for bioorganic phosphates.
# J. Chem. Theo. Comput. 8:4405-4412, 2012.

...hope this helps.....dac

p.s.: I assume you know that it is quite unusual to have a fully protonated
phosphate group. You need either very low pH or an unusal environment.

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Received on Mon Nov 21 2016 - 06:30:05 PST
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