GROMACS version:2023.1
GROMACS modification: No
Hi everyone! I have been trying to simulate a boron nitride nanosheet using charmm36 force field on GROMACS. I have tried various approches but the error persisted
Can not find forcefield for atom H-1 with 18 bonds …
Can not find forcefield for atom H-96 with 22 bonds…
I created the structure of boron nitride using guass view and saved it in pdb format then converted it into gro file using ```
editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90
1H H 2 4.181 2.995 3.500 0.0000 0.0000 0.0000
1H H 3 4.182 3.248 3.500 0.0000 0.0000 0.0000
2B B 4 3.791 3.249 3.500 0.0000 0.0000 0.0000
2B B 5 3.791 2.997 3.500 0.0000 0.0000 0.0000
2B B 6 3.573 3.122 3.500 0.0000 0.0000 0.0000
2B B 7 4.009 3.123 3.500 0.0000 0.0000 0.0000
2B B 8 4.009 2.872 3.500 0.0000 0.0000 0.0000
2B B 9 3.794 2.746 3.500 0.0000 0.0000 0.0000
2B B 10 3.575 2.870 3.500 0.0000 0.0000 0.0000
2B B 11 3.355 2.995 3.500 0.0000 0.0000 0.0000
2B B 12 3.354 3.248 3.500 0.0000 0.0000 0.0000
2B B 13 3.572 3.374 3.500 0.0000 0.0000 0.0000
2B B 14 3.791 3.500 3.500 0.0000 0.0000 0.0000
2B B 15 4.009 3.374 3.500 0.0000 0.0000 0.0000
3N N 16 3.864 3.374 3.500 0.0000 0.0000 0.0000
3N N 17 3.864 3.123 3.500 0.0000 0.0000 0.0000
3N N 18 4.082 3.248 3.500 0.0000 0.0000 0.0000
3N N 19 3.645 3.500 3.500 0.0000 0.0000 0.0000
3N N 20 3.645 3.248 3.500 0.0000 0.0000 0.0000
3N N 21 3.427 3.374 3.500 0.0000 0.0000 0.0000
I think the problem is with the pdb file as i tired to create boron nitride latter with gmx genconf -f xyz.gro -o xyz_sheet.gro -nbox 15 10 1 and it turned out be different from the previous one when i tried to used this gro file to create the topology file no error occurred here a snippet from it.
1GRA N 1 0.061 0.071 0.000 0.0000 0.0000 0.0000
1GRA B 2 0.184 0.142 0.000 0.0000 0.0000 0.0000
1GRA N 3 0.184 0.284 0.000 0.0000 0.0000 0.0000
1GRA B 4 0.061 0.355 0.000 0.0000 0.0000 0.0000
2GRA N 5 0.061 0.497 0.000 0.0000 0.0000 0.0000
2GRA B 6 0.184 0.568 0.000 0.0000 0.0000 0.0000
2GRA N 7 0.184 0.710 0.000 0.0000 0.0000 0.0000
2GRA B 8 0.061 0.781 0.000 0.0000 0.0000 0.0000
3GRA N 9 0.061 0.923 0.000 0.0000 0.0000 0.0000
3GRA B 10 0.184 0.994 0.000 0.0000 0.0000 0.0000
3GRA N 11 0.184 1.136 0.000 0.0000 0.0000 0.0000
3GRA B 12 0.061 1.207 0.000 0.0000 0.0000 0.0000
4GRA N 13 0.061 1.349 0.000 0.0000 0.0000 0.0000
4GRA B 14 0.184 1.420 0.000 0.0000 0.0000 0.0000
4GRA N 15 0.184 1.562 0.000 0.0000 0.0000 0.0000
4GRA B 16 0.061 1.633 0.000 0.0000 0.0000 0.0000
5GRA N 17 0.061 1.775 0.000 0.0000 0.0000 0.0000
5GRA B 18 0.184 1.846 0.000 0.0000 0.0000 0.0000
5GRA N 19 0.184 1.988 0.000 0.0000 0.0000 0.0000
5GRA B 20 0.061 2.059 0.000 0.0000 0.0000 0.0000
6GRA N 21 0.061 2.201 0.000 0.0000 0.0000 0.0000
see how there is alternate arrangement of boron and nitrogen but both the gro file appear fine in VMD still with one I am able to obtain topology but not with the other.Can some one please guide be how can I obtain a suitable pdb/gro file for boron nitride.
SECOND PROBLEM; the next problem is the definition of new atom type I defined new atom type for boron and nitrogen and copy pasted them in the ffbonded and ffnonbonded parameter file along with atp file,but apparently the force field is not recognizing the atom types am I doing something wrong? What is the most appropriate way of defining new atom types in force field?