[gmx-users] Issue regarding MN+2

[RAHUL SURESH]

Yup.. they are available.. literature should help in that.

On Sat, 30 Dec 2017 at 10:53 AM, Amir Zeb <zebamir85 at gmail.com> wrote:

> Alright Dr. Justin,
>
> Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
> you haven't included in the port?
> I'm searching the literature too to find something worthy.
>
> Thanks!
>
> ~Amir
>
> On Fri, Dec 29, 2017 at 8:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 12/29/17 10:39 AM, Amir Zeb wrote:
> >
> >> Thanks Dr. Justin.
> >>
> >> I didn't add this stuff by my own.
> >> I have created Mn+2 topology by simple pdb2gmx command.
> >>
> >
> > Someone hacked your files and added it at some point. None of the
> releases
> > of the C36 port that I have ever made had contained Mn2+ parameters.
> There
> > are CHARMM-compatible parameters that could be added as part of a larger
> > metal parameter set, but they've never been included in the port.
> >
> > Regardless, that's what you need to do - add the correct sigma and
> epsilon
> > values to ffnonbonded.itp for the MN atom type.
> >
> > -Justin
> >
> >
> > ~Amir
> >>
> >> On Dec 30, 2017 12:21 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> >>
> >>
> >>> On 12/29/17 10:11 AM, Amir Zeb wrote:
> >>>
> >>> Hello dear gromacs users,
> >>>>
> >>>> I want to simulate a protein which has two Mn+2 ions as co-factor.
> >>>> Till the solvation, I could prepare the system, but at neutralization
> >>>> step,
> >>>> grompp gives me this fatal error.
> >>>>
> >>>> Fatal error:
> >>>> Atomtype MN not found
> >>>>
> >>>> My system has this topology for Mn+2:
> >>>>
> >>>> [ moleculetype ]
> >>>> ; Name            nrexcl
> >>>> Other_chain_C2      3
> >>>>
> >>>> [ atoms ]
> >>>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> >>>> typeB
> >>>>     chargeB      massB
> >>>> ; residue 501 MN2  rtp MN   q +2.0
> >>>>        1        MN     501    MN2      MN      1          2      54.94
> >>>>  ;
> >>>> qtot 2
> >>>> ; residue 502 MN2  rtp MN   q +2.0
> >>>>        2        MN     502    MN2      MN      2          2      54.94
> >>>>  ;
> >>>> qtot 4
> >>>>
> >>>>
> >>>> And the Mn+2 has this configuration:
> >>>>
> >>>>     501MN2     MN 4551   5.405   5.564   2.987
> >>>>     502MN2     MN 4552   5.582   5.590   3.497
> >>>>
> >>>> I have used Charmm36 ff, and the gromacs version is 5.0.6
> >>>>
> >>>> Please let me know how can I fix this issue?
> >>>>
> >>>> This is not a standard CHARMM atom type - did you add it yourself? If
> >>> so,
> >>> what was the source of the parameters? It looks like you have a residue
> >>> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
> >>> actually have parameters assigned for the atom type in ffnonbonded.itp.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Assistant Professor
> >>> Virginia Tech Department of Biochemistry
> >>>
> >>> 303 Engel Hall
> >>> 340 West Campus Dr.
> >>> Blacksburg, VA 24061
> >>>
> >>> jalemkul at vt.edu | (540) 231-3129
> >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>>
> >>> ==================================================
> >>>
> >>> --
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> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*