lammps-users Digest, Vol 94, Issue 40

Liu Xuepeng,

Open your *.pdb file in VMD and use "topotools writelammpsdata file" and
you should get a data file that is usable, but imperfect. You'll have
to use a text editor to extract (copy/paste) the "ATOMS" and/ or
"BONDS/ANGLES/etc." sections to a spreadsheet (or otherwise) and
introduce (or correct) the necessary missing components (atom_type,
charge, bonds, angles, etc.). This little bit of effort is almost always
easier than creating the data file from scratch (and probably why
topotools was written). When you are done with your edits, paste these
sections back into your lammpsdata file. Detailed documentation for
topotools is available online. Google will find it.

This information is provided so that others with a similar question can
search the archive and find a starting point for a solution and/ or
solve their input file issues. As has been said previously, there is no
"magic bullet" that converts a *.pdb file to file. It's a
multi-step process that has been addressed in previous lammps digest
posts (and one post that occurred only two posts before this one).

Good Luck,