AMBER: MD simulations with Pt atom - how to keep square planar geometry?

From: Pablo Englebienne <>
Date: Wed, 7 Nov 2007 21:21:21 -0500

I'm trying to run MD simulations on a system comprised of a DNA
molecule and a platinum complex, and for that I developed ad-hoc
parameters for the Pt atom by fitting energy values from DFT
(B3LYP/LACV3P**++). I added all the parameters on an frcmod file read
by leap and I'm able to _run_ minimizations and MDs with sander,
although not as satisifactorily as I wish to.

The _only_ problem is that the square planar geometry around the Pt
atom is not stable, and the ligands bend towards a tetrahedral-like
geometry (whether minimizing or running an MD simulation).

I have 2 pointers to this issue:
1) when trying to fit the DFT energies to the MM, it was found that
the 90 degree angles for the ligands were enough to describe the
variance in energy, so the 180 degree N-Pt-N angles have a constant of
2) when trying to fit an oop/improper torsion parameter for the Pt
atom, I found that the variation in MM energies (due to increases in
bond distances and angles) was much larger than the one observed in
DFT, so I (initially) set it to 0.

I tried 2 ways to fix this issue:
1) setting a non-zero Pt oop (actually, 2 sets of oop's, involving the
Pt atom and 2 sets of 3 N atoms bound to it). It appears that leap
does not use it in any case, because the central atom is not a
tricoordinate atom, and it doesn't appear used in the parm file
generated by leap ( After an md simulation in vacuo,
the Pt is still bent.
2) using a pair of dummy atoms bound to the Pt in the axial positions
of the square, with angles at 90 degrees of each of the N substituents
with a high K; a 1A bond distance with a high K; torsions specified
but at 0; and 0 vdW parameters and mass. After an md simulation in
vacuo, the Pt is planar, but the dummy atoms are at 33A from the Pt,
and the simulation crashes with a SANDER BOMB (and the bond energy
goes to the roof).

I'm attaching the files I'm talking about (frcmod; .crd and .top for
both dummy and non-dummy test cases; sander input file as

I'll appreciate any suggestions as to what can I do to keep the Pt in
a square planar geometry...

Thanks for your time in advance!
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382
"Progress is made by lazy men looking for easier ways to do things." -
Robert A. Heinlein

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Sun Nov 11 2007 - 06:07:18 PST
Custom Search