[gmx-users] Issue regarding MN+2

[Amir Zeb]

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?

~Amir