Re: [AMBER] Distorted and Failed Phosphate Simulations

From: Karl Kirschner <>
Date: Fri, 20 Nov 2015 10:36:16 +0100

Hello again,

I had some time and took a detailed look at HF/6-31G(d)'s H2PO4(-) most
stable conformation. I performed constraint optimization for all of the
unique bond, angles, and the ho-oh-p5-oh torsions at HF/6-31G(d) (132
calculations total) to generate potential energy curves for each. Charges
were computed to be balanced with Amber's protein residues. Following
Dave's suggestion, if I increase the each of the angle constants that are
listed in GAFF by 15 kcal/mol rad^2 (+10 kcal/mol rad^2 to each was
sufficient) to the following values, then I am able to perform all of the
equivalent MM optimization (i.e. none of them erroneously stop):

ho-oh-p5 70.88 110.14
o -p5-o 61.01 115.80
o -p5-oh 58.79 115.26
oh-p5-oh 59.58 102.45

However, the resulting MM curves are not in good agreement with the
HF/6-31G(d) target values, as can be seen by the two attached
representative figures that are labeled according to antechamber's assigned
atom types. Both the energies and the geometries are not in good agreement.
The MM angle curve is a discontinuous curve since the ho-oh-p5-oh torsion
changes as the angle bends (the QM is a continuous curve). One could argue
that the QM theory level is not good enough to model H2PO4(-), but I think
it is good enough to illustrate that this system will require careful
parameterization if you are concerned about its conformations during MD

I also modified the ho atom type's Lennard-Jones parameters to those of
Glycam06j (i.e. ho: 0.2000 0.0300), but was unable to perform many of the
MM optimization while using the default GAFF angles parameters.


On Thu, Nov 19, 2015 at 2:26 PM, David A Case <>

> On Thu, Nov 19, 2015, Sigurd Friis Truelsen wrote:
> >
> > I have problems running regular MD simulations with inorganic
> > phosphate HPO4(2-), H3PO4(-) and H3PO4 .
> A "typical" problem with protonated phosphates is that a hydrogen can be
> attracted to a neighboring oxygen on the same phosphate, and there is no
> Lennard-Jones term on the hydrogen to prevent it from collapsing onto the
> oxygen. I'm not sure whether this is the cause of your problems or not,
> but
> you should monitor MD or minimzation carefully to look for such
> interactions.
> Although it is a kludge, it generally works to increase the O--P--O and
> P--O--H angle force constants to enforce a conventional geometry about the
> phorphorus and prevent such intramolecular H--O interactions from ocurring.
> Take a look at the frcmod.phosaa10 file (in $AMBEHROME/dat/leap/parm),
> which
> has parameters we use for phosphorylated amino acids, along with comments
> about how the angle parameters were determined. A similar strategy is
> likely
> to work for phosphate itself.
> ...dac
> _______________________________________________
> AMBER mailing list

Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany

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Received on Fri Nov 20 2015 - 02:00:03 PST
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