[lammps-users] How to convert a pdb file to LAMMPS input data file by using pizza.py?

Dear all

I am a new user pizza.py. I want to convert a pdb file to LAMMPS input data file, my pdb file consists of one protein,one carbon nanotube and specified namber of water molecules. application potential is charmm.
which tools of pizza is applicable for this porpose?

Thanks a lot


what you want to do is not a simple "conversion" process.
the PDB file is missing a lot of information that is required
to simulate your kind of system successfully.
what you have to do is to is "building a topology", i.e.:

- identify each atom's atom type within the CHARMM force
  field and determine its partial charge and mass.
  for proteins that is typically done by matching individual
  residues with a topology database and then mapping
  atom names (following PDB naming conventions) to
  the atom types and their corresponding partial charges.
  for water, this is typically done "manually" with a script.
  for a CNT you'd definitely have to do this manually, since
  there is no way to use the "residue mechanism" for it.

- determine the connectivity, i.e. bond, angles, dihedrals
  and impropers. for proteins, this information is typically
  available per residue in the topology database. for
  water it is easy, the CNT is straightforward to do, but
  might require a little bit of scripting.

- decide how to exactly model the CNT. there are no
  predefined parameters for CNT in charmm. people
  have used phenyl ring parameters successfully, but
  the model of the CNT is pretty simplistic. with LAMMPS
  you have access to better models for CNTs, e.g. with
  AIREBO or Tersoff. you could then use pair_style hybrid
  to combine it with the rest.

this is best done for protein, water and nanotube separately.
and then merging those pieces later. for the protein you
would need either the charmm software or the psfgen tool
from NAMD to build a suitable .psf topology file. for the
rest you could do some charmm scripting or use the
topotools package in VMD. the latter follows some simple
rules and uses no database, so you have to look up
atom types manually and set them. you could also use
it to merge the pieces and export it to a data file.


The PDB tool in Pizza.py does something different. It takes a dump
file (LAMMPS output)
and an existing PDB file, and replaces the coords in the PDB with the
coords in each
dump snapshot, to create a series of PDB files for viz, by something like VMD.

If you want to convert a PDB file into a LAMMPS input data file, you can
use the tools/ch2lmp tool, but you also need force field and other info,
as Axel mentioned.


Dear Steve

I convert one pdb file (a specified protein consists of three chains) to three *.psf by using psfgen tools on VMD. by using charmm2lammps tools and also charmm force field i convert them to three data files. Now i need to merge them together and have one data file. How to do merge them together? do there is any software or tools that to merge them to a single data file?