How to using amber2lammps program?

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1

Dear Developers and Users,

I have used charmm2lammps from tools directory already. Now, I want to
use amber2lammps to convert pdb files to lammps input and data files.
But, there are not a suitable instruction for using this program
amber2lammps. Also, I am not familiar with amber codes. Is there
anybody who knows how can I run a pdb file with AMBER forcefield in
lammps?

Thanks a lot,
Farrokh

2

Amber2lammps is a pretty old tool, and not well-supported
in LAMMPS, due to lack of use. Hopefully someone on
the mail list will have ideas for you.

Steve

3

Amber2lammps convert the files from amber format (.top .crd) to lammps input format. It does not use pdb as input. You need to use amber to read in pdb and create .top (connectivity info) and .crd (cordinates) files. The .top file also have force field information. you will need to assign a force field (different force field files should be in some /leap/dat directory) to create .top and .crd files. amber2lammps.py should take care of the rest. I myself successfully converted some files recently.

good luck.