[gmx-users] Issue regarding MN+2

[Amir Zeb]

Thanks Dr. Justin.

I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.

~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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