[gmx-users] Atomtype ZN2+ not found
Shankar Prasad Kanaujia
spkanaujia at gmail.com
Sat Dec 20 04:32:29 CET 2014
Thanks for the details. As you mentioned, I did not find any force field
which contains parameters for all metals.
On Fri, Dec 19, 2014 at 5:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> Cu2+ Cu2+ 29 63.54600 2.000 A 2.08470e-01
> Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01
> Zn2+ Zn2+ 30 65.37000 2.000 A 1.95200e-01
> Ar Ar 18 39.94800 0.000 A 3.41000e-01
> 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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Shankar Prasad Kanaujia, Ph.D.
Department of Biotechnology
Indian Institute of Technology Guwahati
Guwahati - 781039 Assam, India
Tele: 0361 258 2228
Fax: 0361 258 2249
Email: spkanaujia at iitg.ernet.in
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