Get the useful data for lammps

Dear all,

I’m doing the simulation of the HAP (hydroxyapatite), I’ve a paper Fracture mechanics of hydroxyapatite single crystals under geometric confinement, in which the simulation uses the CHARMM force field. In the manual of LAMMPS, the force field need the bond, angle, dihedral list. Someone told me that I can use the topotools in VMD to realize it, but I just have a hydroxyapatite document in PDB format by the Material Studio, by which I cannot get the data contain the angle, dihedral list. I want to know how to get the bond, angle, dihedral list?

Dear all,

I'm doing the simulation of the HAP (hydroxyapatite), I've a paper Fracture
mechanics of hydroxyapatite single crystals under geometric confinement, in
which the simulation uses the CHARMM force field. In the manual of LAMMPS,
the force field need the bond, angle, dihedral list. Someone told me that I
can use the topotools in VMD to realize it, but I just have a hydroxyapatite
document in PDB format by the Material Studio, by which I cannot get the
data contain the angle, dihedral list. I want to know how to get the bond,
angle, dihedral list?

you could use topotools for that (see its documentation:
Homepage of Axel Kohlmeyer - TopoTools ), but it
may need some additional touch ups, if you want to model a fully
periodic crystal with bonds across the periodic boundaries (which is
not supported in any automated tool i know). in that case, it is
probably best to write a little tool yourself that would generate the
data file according to your needs. for a system with a small unit
cell, this would be a rather straightforward process (and if you do,
don't forget to submit it for inclusion into the LAMMPS tools folder,
because there may be others, that would benefit from it as well).

axel.

If you just want to visualize the system in VMD with bond info, you can save your system in .mdf and .car format and see it with all the associated topology. .mdf format contains topology info. You can also convert it to lammps format with msi2lmp tool and then visualize the lammps file with topotools plugin with same bonded topology.

Regards
Vikas