[gmx-users] Atomtype ZN2+ not found

Justin Lemkul jalemkul at vt.edu
Fri Dec 19 13:17:11 CET 2014

On 12/19/14 2:59 AM, Shankar Prasad Kanaujia wrote:
> Dear users,
> I had simulated one protein with metal Zn (Zinc) bound using Gromacs
> version 4.5.5 with OPLSS-AA force field. Now, I am trying to rerun to
> calculate the energy between two groups with Gromacs version 5.0.2. I am
> getting the following error:
> Atomtype ZN2+ not found.

Zn2+ and some other ions were removed from the OPLS-AA files because they were 
not, in fact, actually OPLS-AA parameters.  Note that this is stated prominently 
in ffnonbonded.itp:

; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added them.
  Cu2+       Cu2+   29   63.54600     2.000       A    2.08470e-01  4.76976e+00
  Fe2+       Fe2+   26   55.84700     2.000       A    2.59400e-01  5.43920e-02
  Zn2+       Zn2+   30   65.37000     2.000       A    1.95200e-01  9.78219e-01
  Ar         Ar     18   39.94800     0.000       A    3.41000e-01  2.74580e-02

I would rigorously evaluate whatever you did with 4.5.5 and consider repeating 
the simulations with better parameters, if they exist, or using a force field 
for which Zn2+ has been parametrized properly.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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