AMBER: Pang-model of Zn2+

From: Oliver Hucke <>
Date: Thu, 25 Mar 2004 17:04:48 -0800

Dear All,

I am wondering if people out there have experience with the Pang
approach to modeling Zn2+ in proteins?

I am using the tetrahedral divalent cation approach of Pang, i.e. the 2
positive charges are distributed on 4 dummy atoms at the apices of a
tetrahedron around the Zn. (Prot. Science, v9, pp. 1857)
One of the ligands of the zinc is a hydroxyl ion. During the
minimization of my system this ion fuses with one of the dummy atoms,
which leads to infinite electrostatic energy.

The fusion seems to happen because the dummy atom has no repulsive van
der Waals properties (r=0) while its distance to the zinc is flexible
(force constant = 540). It moves from its equilibrium distance from the
Zn (0.9A) to a distance close to the r-value of the oxygen (1.7A). This
comes with a penalty in bond energy dummy-zinc but the electrostatics
overcome this barrier.

Has anybody encountered similar problems with this Zn2+ model?
What is the reasonable behind a flexible zinc dummy distance? Would it
not be better to fix this distance?

Best regards,

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email:
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Received on Fri Mar 26 2004 - 01:53:00 PST
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