[gmx-users] Issue regarding MN+2

[Justin Lemkul]

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

==================================================