[gmx-users] Atomtype ZN2+ not found

[Shankar Prasad Kanaujia]

Dear Justin,

Thanks for the details. As you mentioned, I did not find any force field
which contains parameters for all metals.

Regards,
Shankar

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
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Shankar Prasad Kanaujia, Ph.D.
Assistant Professor
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
Homepage: http://www.iitg.ernet.in/spkanaujia/