AMBER Archive (2006)

Subject: Re: AMBER: Atoms overlapping

From: Thomas Steinbrecher (
Date: Mon Dec 11 2006 - 16:11:47 CST

Dear Nitin,

in a simulation of a protein containing a protonated ADP molecule I ran
into similar troubles as you before. My solution to this was to build a
frcmod file that contained to new atom types to describe a P-O-H

It contained parameters modelled partly from the ones Heather Carlson used
in Meagher et al. J Comp Chem, 24, 1016-1025.

In my opinion adding just a vdW parameters for H is not going to be
enough, I am pretty sure you will need an angle parameter too. This is
because hydrogens are small (vdW-wise) but in a phosphate setup, they
might have large positive partial charges next to large negative ones on
the oxygens.

In my simulation I added types OX and HX, with these bond/angle parms:

ox-hx 525.0 1.480
hx-ox 553.0 0.946

ox-p-ox 45.0 101.31
hx-ox-p 45.0 106.31

potentials were taken by analogy from similar fragments, geometries from
an energyminimized h2po4 molecule. Suprisingly, no dihedral potential was
necessary, because the potential for rotation around an h-o-p-o dihedral
with these parameters is reasonably accurate when compared to a HF6-31G*
QM calculation.

You can experiment a little with vdWparameters for the H, but I would
assume that you can keep the zero ones from ho.

This worked well for me, but I never did in-depth testing on how realistic
this potential model is.

> h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963

vdW-radius is the first number, potential well depth the other.


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