Converting packmol output to lammps data file

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1

Dear all,

I am having some trouble when converting a somewhat complex system from the packmol output to lammps data file using vmd.

I’ve seen Axel’s tutorials, but I still could not produce an usable data file.

The system is a solid phase material composed by 2 different molecules inside a cube of 20x20x20. This cube goes inside a 40x40x40 cube where additional 1000 oxygen molecules are added. In the final system, there are 5 different elements.

So, I have the .pdb file for the final structure, but when converting to lammps data file and reading the vmd output, all atoms(elements) are changed.

Is there a way of avoiding this change? Or I’ll have to do 4 different scripts in vmd (like the ones from Axel’s tutorials) and try to assemble the system?

Thank you.

Rene

2

This sounds like an issue with your PDB file.

Have you checked whether the atom names in the PDB file generated by
packmol are correct? If not then perhaps you should check the atom
names in the original PDB files that you fed to packmol. Alternately,
if your packmol's INP file reads the coordinates in a different format
(.xyz files) and saves the result in a PDB file, the resulting PDB
file could have weird atom type names.

This may not be relevant, but have you checked the order of the atoms
in your PDB file for the final structure? (I vaguely recall that
older versions of packmol printed the atoms out in a different order
than the current versions of packmol. I think that in older versions
of packmol, it would print out the list of molecules in a mixture in
alternating order. In order to make it work with moltemplate, I asked
Leandro to change it so that it would list the coordinates of all the
oxygen molecules consecutively, followed by all the water molecules,
consecutively, and all instances of next type of molecule
consecutively etc... This could be irrelevant. I'm not sure if atom
order matters in topotools.)

Cheers
Andrew

3

Dear Andrew,

Thanks for the info. I have checked the PDB files and they are all correct. The most recent packmol version was installed to avoid the issue you mentioned.

When I open the PDB file generated by packmol in VMD, all atoms are correctly identified. When using topotools to write lammps data file (and then reading the generated file in VMD), some elements are changed (carbon becomes nitrogen, hydrogen becomes carbon etc.).

I am confused by what could be the problem, as it seems that VMD is not translating correctly the bonds lenghts. Is there any other procedure in VMD to avoid this issue?

Thanks

Rene

4

Dear Andrew,

Thanks for the info. I have checked the PDB files and they are all
correct. The most recent packmol version was installed to avoid the issue
you mentioned.

When I open the PDB file generated by packmol in VMD, all atoms are
correctly identified. When using topotools to write lammps data file (and
then reading the generated file in VMD), some elements are changed (carbon
becomes nitrogen, hydrogen becomes carbon etc.).

I am confused by what could be the problem, as it seems that VMD is not
translating correctly the bonds lenghts. Is there any other procedure in
VMD to avoid this issue?

​this seems to be a VMD/TopoTools issue and should thus be discussed on the
VMD mailing list, not here.
also, without knowing the individual steps you did in detail to do the
conversion and providing a suitable (small) example file, it will be
difficult to provide meaningful suggestions.

axel.