Dear LAMMPS users,
I tried to use the charmm to lammps conversion tool to generate LAMMPS data file from the pdb and psf file of an organic molecule that I am working on. I found out that the tool didn’t detect the two oxygen atom types (OH1 and a user-defined type, OET) in the pdb and psf files it was supplied. This is what the data file looks like:
LAMMPS data file. CGCMM Style. atom_style full. Created by charmm2lammps v1.9.1 on Fri Jun 15 12:48:40 CDT 2018
3480 atoms
3480 bonds
5640 angles
7680 dihedrals
0 impropers
8 atom types
13 bond types
23 angle types
34 dihedral types
0 improper types
-53.7725 53.7725 xlo xhi
-49.03 49.03 ylo yhi
-45.1055 45.1055 zlo zhi
Masses
1 0 #
2 1.008 # H
3 1.008 # HA
4 1.008 # HP
5 12.011 # CA
6 12.011 # CT1
7 12.011 # CT2
8 12.011 # CT3
Pair Coeffs # lj/charmm/coul/long
2 0.046 0.400013524445 0.046 0.400013524445 # H
3 0.022 2.35197261589 0.022 2.35197261589 # HA
4 0.03 2.42003727796 0.03 2.42003727796 # HP
5 0.07 3.55005321205 0.07 3.55005321205 # CA
6 0.02 4.05358916754 0.01 3.38541512893 # CT1
7 0.055 3.87540942391 0.01 3.38541512893 # CT2
8 0.08 3.67050271874 0.01 3.38541512893 # CT3
Please what should I do to remedy this? Thank you.