[lammps-users] pdb file format

hi
I wrote a program to generate a novel nanostructure . i want to write the structure in pdb file format but I cant find the exact format to use it with matlab programming.
I use fprintf command to write the datas in text file.
can anybody help me with this?
thanks.
omid.

hi
I wrote a program to generate a novel nanostructure . i want to write the structure in pdb file format but I cant find the exact format to use it with matlab programming.
I use fprintf command to write the datas in text file.
can anybody help me with this?
thanks.
omid.

Why are you posting this question on the LAMMPS mailing list?
Are you trying to use this PDB file to build a system that you intend to simulate using LAMMPS?
If that is your goal, then be warned: I am not aware of any free software that can automatically read PDB files and automatically convert them into LAMMPS “input” and “data” files. (Although VMD/topotools can read PDB files and generate bonds, angles, dihedrals, and impropers. EMC can read PDB files, but I am not familiar enough to say more. Moltemplate only reads the X,Y,Z coordinates in the PDB file and discards the other information.)

If you wrote a program to create a novel structure, I suggest that instead of creating PDB files, create a LAMMPS “data” file instead.
You can familiarize yourself with the LAMMPS “data” file format here:
https://lammps.sandia.gov/doc/2001/data_format.html

Also: There is a list of software that can generate LAMMPS data files here:
https://lammps.sandia.gov/prepost.html
Many of these programs have their own file formats which might also be worth considering.

Andrew