I used ch2lmp tool (charm2lammps.pl) to make “data file” from my pbd, psf, topology and parameter files by typing the script " perl charmm2lammps.pl all27_prot_lipid_na kcsav -charmm -border=1 -pdb_ctrl -water -ions " . This command makes some files such as “Data File” and “in file”. However, when I use the “in file” by LAMMPS, this error is occured:
"Finding 1-2 1-3 1-4 neighbors …
6 = max # of 1-2 neighbors
20 = max # of 1-3 neighbors
ERROR on proc 0: 1-3 bond count is inconsistent
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 "
I have used different pdb files (proteins and membranes). But I always faced this error.
Does this error refer to “data file”? If yes, what should I do to overcome this problem? How about the other files (pdb, psf, prm or top)? It should be noted that the “data file” is created by the ch2lammps tool without any errors and I use that file without any changes.