Hello to All,
When converting a pdb. file (generated by Materials Studio) of polymer model(PE,PLA) into lammps data file by VMD topo tools, there's too many atom types in the output file(lammps data file). What could I do to reduce the atom types in lammps data file?
In PLA.pdb, every atom has a unique name, hence a unique atom type in pla.data, and all monomers are grouped into one monomer, residue ID 1; and all chain have the same chain ID, L. This is not a standard way to represent a polymeric system composed of multiple chains. PE.pdb looks better but lacks chain identifiers and separators (TER).
As a side note: CONECT section in PLA.pdb is incorrect, linking atoms that should not be linked.
Thanks Martin Klvana ,
I'm more clear now. The PLA model is built by Amorphous Cell function and optimized by Forcite Molecular Dynamics. I guess I shouldn't further optimize it to avoid the linkings.
As for the converting part, do you have any suggests to include chain identifiers and separators (TER) in Lammps data file?
Groups can be defined in LAMMPS with group command. TER mark is for PDB files.
https://docs.lammps.org/group.html
Hi Zhe Wang ,
Would you mind sharing more details about how to use Ovito to convert the pdb. file to the data file? I have tried with my Ovito, it couldn't recognize nor open my pdb. file.
You can also use the OpenBabel free software..It is easy to use. choose lmpdat for the output format.
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