Dear LAMMPS users,
I ran into a problem with the ch2lmp tool, and thought I would post here before contacting the authors of the tool. Following the example folder provided by the authors, one builds 1ac7.data from a psf file. I noticed, however, that the number of dihedrals listed in the psf file (1497) is inconsistent with the number of dihedrals in the lammps data file (1659). Despite this inconsistency, the data file still seems to work well with LAMMPS, although I’m unsure if it is the same structure as in the psf (perhaps it is the same, and the number was such that some dihedral ids were skipped?).
Second, I tried using the charmm2lammps tool on 1d3z pdb. I generated the psf using psfgen, as instructed in the readme file, vmd commands listed below. This psf contained 1231 atoms, 1242 bonds, 2257 angles, 3293 dihedrals, 205 impropers and 74 cross terms. When I used the charmm2lammps tool, however, a LAMMPS data file was created with 1231 atoms, 1242 bonds, 2257 angles, 3428 dihedrals, 202 impropers (not sure about cross terms). When I attempt to use this data file in a lammps simulation, I receive an error: “1-3 bond count inconsistent”
So my first question is, can the example provided in ch2lmp be trusted? and second, having understood the dihedral numbering, what is wrong with 1d3z, perhaps a missing improper?
Please let me know if I haven’t provided enough information.