[gmx-users] Issue regarding MN+2
zebamir85 at gmail.com
Fri Dec 29 16:11:08 CET 2017
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.
Atomtype MN not found
My system has this topology for Mn+2:
[ moleculetype ]
; Name nrexcl
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
; residue 501 MN2 rtp MN q +2.0
1 MN 501 MN2 MN 1 2 54.94 ;
; residue 502 MN2 rtp MN q +2.0
2 MN 502 MN2 MN 2 2 54.94 ;
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?
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