[gmx-users] Topology file

[Salman Zarrini]

Dear all,
I want to create a topol.top file for Silica slab for which the force
fields parameters are available in literature as well as in the lammps.data
file which works fine in lammps (below links). The slab has in general 2184
atom including two types of O atom(OS in surface part and OB in the bulk
part), one Si type and one hydrogen type HS. The gro file can be found in
the below link.

*.gro file*
https://drive.google.com/open?id=1BMdNcqaSIxkMMr89VzUmrIGQOZlusaG0

*lammps.data file*
https://drive.google.com/open?id=1Aqpyv4Mc3VEZGGYaxEuOpbdizVpbs5xR

Would you please help me set up the topol.top file for such system?

For starting, I have prepared the the below topol.top file by considering
the unit conversion and and other cures, however I do not know where I am
doing wrong that causes mismatching between some atoms in gro file and in
topol file as the first error.

One possible approach might be to include all the atoms, bonds and angles
directly in the [ atom ], [ bonds ] and [ angles ] sections of topol.top,
respectively, but that would be so frustrating.

;%%%%%*  topol.top* %%%%%%%%%%

#include "gromos54a7.ff/forcefield.itp"

[ atomtypes ]
;   name      mass        charge    ptype
sigma                      epsilon
    OB       15.999400    -0.550        A
0.30914185519469770             0.226087102152
    OS       15.999400    -0.675        A
0.30914185519469770             0.510789378936
    Si         28.086000    +1.100       A
0.36972296802824080             0.389372231484
    HS        1.0080000    +0.400       A
0.09666251091822681             0.062801972820

[ moleculetype ]
; molname       nrexcl
GF             3

[ atoms ]
;id at_type    res_nr  residu_name    at_name         cgnr      charge
1     OB          1       GF            OB             1       -0.550
15.999400
2     OS          1       GF            OS             1       -0.675
15.999400
3     Si            1       GF            Si               1       +1.100
28.086000
4     HS           1       GF            HS             1       +0.400
1.0080000

[ bonds ]
; i     j       funct   length          force.c.
1       3       1       0.16800  238647.49671600002     ;;OB-Si
2       3       1       0.16800  238647.49671600000     ;;OS-Si
2       4       1       0.09450  414493.02061199996     ;;OS-HS

[ angles ]
; i     j       k       funct   angle      force.c.
2       3       1       1       109.500  837.3596376    ;; OS-Si-OB
1       3       1       1       109.500  837.3596376    ;; OB-Si-OB
3       1       3       1       149.000  837.3596376    ;; Si-OB-Si
3       2       4       1       115.000  418.6798188    ;; Si-OS-HS

[ system ]
; Name
GF

[ molecules ]
GF           546             ;;; 546*4 = 2184 atoms in gro file

;%%%%%%%%%%%%%%%

Thank you.
Salman