In our current project, we are attempting to simulate BN sheets using the Gromacs package. However, we have a problem introducing BN in Gromacs.
Based on Gromacs manual, we added a new residue file (BN) in .rtp file of forcefield GROMOS53a6 as follows:
[ BN ]
[ atoms ]
B NR 0.000 0
[ bonds ]
B NR gb_53
[ angles ]
B NR B ga_54
NR B NR ga_55
[ impropers ]
B NR B NR gd_42
New atom type B and Lennard-Jones parameters have been attached to atomtypes.atp and ffnonbonded.itp files, respectively. B-N bonding information has been added to ffbonded.itp. The new residue (BN) has been introduced to residuetypes.dat and B-N special bond line has been increased in specbond.dat file as follows:
BN B 1 BN N 1 0.1446 BN BN
When we use the Pdb2gmx command to make a .top file from a .pdb file. We receive this warning:
Problem with chain definition or missing terminal residues. This chain does not appear to contain a recognized chain molecule.
The .top has been produced with two atoms including B and NR(N aromatic). It is supposed that the force field can’t distinguish the connectivity between the residues and consider the structure as a chain. We appreciate your kindness if you could give us a hint on how to solve this error. Do you think this procedure is appropriate to model BN sheets?