[gmx-users] Cationic Dummy atom method

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 04:25:14 CET 2014

On 2/19/14, 3:24 PM, Williams Ernesto Miranda Delgado wrote:
> 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
> output:
> 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?

Both outcomes indicate an unstable topology, but without seeing it, it's 
impossible to suggest what might be wrong.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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