Thanks Andrew for your very helpful comments. I used the topotools and I found it very helpful for creating data file. However, since I could not create a pdb file containing those bonds crossing the boundaries (I used Avagadro and Mercury and both did not keep those bonds when converting cif file to pdb file) finally I wrote a script to convert cif file to lammps data file.
Yet I would like to know if anyone is aware of a tool which can create bonds across the boundaries. Do topotools and Moltemplate have such a capability?
Best,
Hasan
Thanks Andrew for your very helpful comments. I used the topotools and I
found it very helpful for creating data file. However, since I could not
create a pdb file containing those bonds crossing the boundaries (I used
Avagadro and Mercury and both did not keep those bonds when converting cif
file to pdb file) finally I wrote a script to convert cif file to lammps
data file.
Yet I would like to know if anyone is aware of a tool which can create bonds
across the boundaries. Do topotools and Moltemplate have such a capability?
topotools can add individual bonds and it doesn't check whether those
wrap around periodic boundaries or not.
however for determining bonds heuristically, it relies on VMD's (fast
and parallel) atom radius based bond search, which does not know
anything about periodic boundaries. for molecular crystals, a strategy
that can work is:
- build your crystal structure so that you have "whole" molecules,
even if the atoms would extend outside the box.
- load the coordinates into VMD, let VMD/topotools guess the bonds and
the rest. set the cell dimensions and write out your data file
- if you absolutely want all atoms to be placed into the principal
cell, use the VMD pbctools plugin to wrap all atoms back. this won't
change the bond topology.
axel.