Adding zinc molecule

User discussions
1

GROMACS version:2023
GROMACS modification: Yes/No

I have been trying to run a simulation with a few added zinc molecules using the insert-molecules function in my gro file with a protein. I get the following note.

In moleculetype ‘LIG’ 1 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.

Prior to the note I get

Atom 1 ‘ZN’ in moleculetype ‘LIG’ is not bound by a potential or constraint to any other atom in the same moleculetype.
Atom 1 ‘ZN’ in moleculetype ‘LIG’ is not bound by a potential or constraint to any other atom in the same moleculetype.

my zinc.gro that I used to insert zinc looks like the following.

7
1LIG     ZN    1   1.289  -1.374   0.227
1LIG      O    2   1.470  -1.363   0.308
1LIG     H1    3   1.493  -1.272   0.322
1LIG     H2    4   1.533  -1.404   0.249
1LIG     O1    5   1.273  -1.596   0.211
1LIG     H3    6   1.189  -1.619   0.172
1LIG     H4    7   1.344  -1.629   0.155

1.00000 1.00000 1.00000

Any suggestion will be greatly appreciated.

My zinc itp file looks like the following

; ----
; Built itp for zinc.mol2
; by user vzoete Sun Mar 19 13:29:44 UTC 2023
; ----
;

[ moleculetype ]
; Name nrexcl
LIG 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 ZINC 1 LIG ZN 1 2.0000 65.3900
2 OH2 1 LIG O 2 -0.8600 15.9994
3 HOH 1 LIG H1 3 0.4300 1.0079
4 HOH 1 LIG H2 4 0.4300 1.0079
5 OH2 1 LIG O1 5 -0.8600 15.9994
6 HOH 1 LIG H3 6 0.4300 1.0079
7 HOH 1 LIG H4 7 0.4300 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
7 5 1 0.09690 474544.3 0.09690 474544.3
6 5 1 0.09690 474544.3 0.09690 474544.3
4 2 1 0.09690 474544.3 0.09690 474544.3
2 3 1 0.09690 474544.3 0.09690 474544.3

;[ pairs ]
; ai aj fu

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
3 2 4 1 103.9780 396.25 103.9780 396.25
6 5 7 1 103.9780 396.25 103.9780 396.25

2

Your situation is the corner case that the note discusses. You may not need a bonded potential between the ion and the two water molecules. It’s unusual and often means the user forgot to do something, but here this is not the case.

3

I removed the following lines from the tip file

2 OH2 1 LIG O 2 -0.8600 15.9994
3 HOH 1 LIG H1 3 0.4300 1.0079
4 HOH 1 LIG H2 4 0.4300 1.0079
5 OH2 1 LIG O1 5 -0.8600 15.9994
6 HOH 1 LIG H3 6 0.4300 1.0079
7 HOH 1 LIG H4 7 0.4300 1.0079

and the following lines from the gro file

1LIG      O    2   1.470  -1.363   0.308
1LIG     H1    3   1.493  -1.272   0.322
1LIG     H2    4   1.533  -1.404   0.249
1LIG     O1    5   1.273  -1.596   0.211
1LIG     H3    6   1.189  -1.619   0.172
1LIG     H4    7   1.344  -1.629   0.155

I also repeated the production by redoing the topology and parameter files by removing two H2O molecules from the input molecule file and with this, I could run the production in both cases without any problem.