[gmx-users] Cationic Dummy atom method

Williams Ernesto Miranda Delgado wmiranda at fbio.uh.cu
Wed Feb 19 21:34:30 CET 2014

Hello Gromacs users
I am trying to simulate a complexed zinc ion with the cationic dummy atom
method (Pang,1999) in Amber FF.
In this Method the Zinc-Ion is mimicked by a central uncharged Zinc (full
mass) atom and 4 tetrahedric dummys with 0.5 charge each and very small
mass (0.1).

I used the force field parameters reported in Pang, 2000 (only bond and
angle parameters reported), but when I performed steepest descendent (sd)
energy minimization of a protein:ligand complex with this zinc dummy
cation in the active site, the tetrahedral geometry got distorted.
On the other hand, when I try to minimize the energy of the system using
the conjugate gradient method (after the sd minimization) I get this

Fatal error:
30491 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.

Could you please give me some advices?
Thank you

Lic. Williams Ernesto Miranda Delgado
Biochemistry and Molecular Biology
Bioinformatics and Biomolecular Dynamics Lab.
Center for Protein Studies
Faculty of Biology, University of Havana
25th Street between I and J, Vedado, Havana

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