[gmx-users] Issue regarding MN+2

[Amir Zeb]

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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>>>
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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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