How to prepare a system
Contents
ParmEd
ParmEd is handful for converting common file formats such as psf/pdb to top/gro (Gromacs) or top/inpcrd (Amber).
import parmed as pmd
gmx = pmd.load_file('topol.top', xyz='system.gro')
gmx.save('system.top', format='amber')
gmx.save('system.inpcrd', format='rst7')
gmx.save('ionized.psf')
Please note that the Gromacs output comes WITHOUT forcefields.
Protein-membrane systems
CHARMM to Gromacs
File conversion from CHARMM to Gromacs is often encountered, because CHARMM-GUI is very convenient for creating a membrane system. There is a script psf2itp provided by CHARMM-GUI (modified by Kev 2019) to convert a psf to topology file for Gromacs with CHARMM36m ff. You may replace the toppar to change the force-field (but still have to be CHARMM). CHARMM36m ff for Gromacs could be downloaded here.
python psf2itp.py toppar.str PSFfile
Protonation states of amino acids
PlayMolecule (Using ProPka)
