[lammps-users] Converting PDBs to LAMMPS Input Format

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1

Does anybody know of a way to convert a PDB file to LAMMPS input format.
My goal is to do the following :-

1) Input a PDB
2) Convert the PDB to LAMMPS input format and use the potential energy
(CHARMm style) code in LAMMPS to compute the energy and gradient of the
protein structure as specified in the PDB.
3) Output the energy and gradient into a file.

Any help will be greatly appreciated.

Thanks,

- Vanitha Suresh

2

Vanitha,

Yes, use the charmm2lammps.pl tool in the tools/ch2lmp
directory of the LAMMPS distribution. Read the
documentation in that folder to help you do the
conversion.

Good luck!

Paul

3

Thanks. The README was very helpful. Do you have tools to convert from PDB
to CRD in Perl or Python. I see that you have a third party FORTRAN code
but I'm not much of a FORTRAN person :slight_smile:

Vanitha,

4

You shouldn't need the crd files at all.
charmm2lammps.pl can use pdb files directly. But I'm
sure there are conversion scripts aplenty out there
that could do the job if you really want the crd files
--- you can use CHARMM itself as well. -Paul