[gmx-users] Issue regarding MN+2

[Alexandr Nasedkin]

On 30/12/2017 06:23, Amir Zeb 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.
Try to start with following papers:

http://pubs.acs.org/doi/abs/10.1021/jp054177x

http://pubs.acs.org/doi/abs/10.1021/ct400055v

http://www.sciencedirect.com/science/article/pii/S0010854517300383

-Alexandr

>
> 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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>> Gromacs Users mailing list
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