Converting PDB file into LAMMPS input file

Hi
I converted pdb file ( “hydroxyapatite” molecule) into lammps input file using command :

writelammpsdata []

but the problem is, it is showing angles=0, diehedrals=0, impropers =0, which should not be the actual case.is there any speciic command in VMD to convert pdb file into lammps input with all angles, diehdrals ??

Thanks
Mahesh

Hi
I converted pdb file ( "hydroxyapatite" molecule) into lammps input file

last i've heard about it, hydroxyapatite was a crystal and not a molecule.

using command :

writelammpsdata <file name> [<atom style>]

but the problem is, it is showing angles=0, diehedrals=0, impropers =0,
which should not be the actual case.

please note that a PDB file usually does *not* include *any* form of
bond topology information, most certainly not angles and dihedrals. it
also is lacking any force field typing or charge information. VMD will
try to guess missing bond information upon loading, if nothing is
present, but since VMD does not regard periodicity for that, this only
works for isolated molecules and for atoms that it can correctly
identify (e.g. not for calcium, which will most likely be recognized
by VMD as peptide alpha carbons.

is there any speciic command in VMD to convert pdb file into lammps input
with all angles, diehdrals ??

you cannot convert what is not there. you will have to specifically
apply force field typing, check bonding and add missing bonds, if
needed, then apply (partial) charges and recreate the missing bond
topology data based on the requirements of your specific choice of
force field.
the data file that VMD writes will still be missing parameter
information, since that cannot be easily included since it is too
force field specific.

please note that this whole process of force field typing should be
well explained in any reasonably detailed book on MD simulations.

axel.