[gmx-users] Issue regarding MN+2
jalemkul at vt.edu
Fri Dec 29 16:21:22 CET 2017
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
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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