My topology file uses atom names for ions, not molecules. I can't see errors?

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1

GROMACS version:gromacs/2023
GROMACS modification: No

I “inherited” a topology file for some simulations I’m running which appear to reference sodium and chloride atom names instead of their molecule names (molecule names appear to me to be Na Cl while atoms are all caps). I’m unsure if this will affect my simulation, as I’ve run simulations and I haven’t seen any errors triggered. However, I obviously want to make sure my simulation is behaving accurately. Would anybody be able to give me feedback about whether my topology file is correctly referencing the ions?

My topology file:

[ defaults ]
; nbfunc        comb-rule       gen-pairs
1               2               no

[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
 cD       cD          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
 hL       hL          0.00000  0.00000   A     2.60142e-01   4.18400e-02 ; 1.46  0.0100
 c        c           0.00000  0.00000   A     3.31521e-01   4.13379e-01 ; 1.86  0.0988
 o        o           0.00000  0.00000   A     3.04812e-01   6.12119e-01 ; 1.71  0.1463
 oh       oh          0.00000  0.00000   A     3.24287e-01   3.89112e-01 ; 1.82  0.0930
 ho       ho          0.00000  0.00000   A     5.37925e-02   1.96648e-02 ; 0.30  0.0047
 OW       OW          0.00000  0.00000   A     3.15075e-01   6.35968e-01 ; 1.77  0.1520
 HW       HW          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000

; Remember to remove incorrect ion parameters from include
; list and edit below molecules section as required.

#include "aqvist_ions.itp"
;#include "merz_ions.itp"
#include "DCA.itp"
#include "DCN.itp"
#include "amber03.ff/tip3p.itp"

[ system ]
DCA and DCN with ions in tip3p water

[ molecules ]
; Names must match those used in included .itp files.
; Order & number of molecules must match structure file.
; Compound        nmols
DCA                144
DCN                144
K                  165
Cl                  21
SOL              11520
~

which are formatted in the pdb file as:


ATOM   9073  NA  Na    289      50.380  49.700   6.010  1.00  0.00            
ATOM   9074  NA  Na    290      44.710   4.890  60.810  1.00  0.00

Here is the ion itp file too:

[ atomtypes ]
; name    at.num    mass    charge ptype  sigma      epsilon
K+            19  39.100000  0.00000000  A     0.47360176    0.001372352
Na+           11  22.990000  0.00000000  A     0.33283976     0.01158968
Cl-           17  35.450000  0.00000000  A     0.34709414        1.10876


[ moleculetype ]
; Name            nrexcl
K          3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB
; residue    1 K rtp K q 1.0
    1         K+      1      K      K      1 1.00000000  39.100000   ; qtot 1.000000


[ moleculetype ]
; Name            nrexcl
NA          3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB
; residue    1 NA rtp NA q 1.0
    1        Na+      1     NA     NA      1 1.00000000  22.990000   ; qtot 1.000000


[ moleculetype ]
; Name            nrexcl
CL          3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB
; residue    1 CL rtp CL q -1.0
    1        Cl-      1     CL     CL      1 -1.00000000  35.450000   ; qtot -1.000000

~
2

The [ molecules ] section in your topology file specifies the number of molecules in the system. The names specified in that section should match the [ moleculetype ] name, which is K, NA, CL in the ion itp file you showed. In your [ molecules ] section Cl is specified. I’d be surprised if gmx grompp would work with that topology. Are you sure that the ion itp file you posted is the same as aqvist_ions.itp?

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