[gmx-users] Issue regarding MN+2

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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