I’ve started my journey into the world of molecular dynamics, and so I’m getting used to the file formats in this field of science.
I needed to convert my
.gro files into
.pdb and this seemed to be tricky to implement until I came across this package called MDAnalysis. It’s a pretty nifty package and is pip installable!
So to start off import
MDAnalysis and initiate a
universe with your Gromacs file as the path.
import MDAnalysis as mda
universe = mda.Universe(path_to_gromacs_file)
Next, we will use the
Writer object from
MDAnalysis with the output file specified with the extension
.pdb . The software is smart enough to know what you’re going for.
with MDAnalysis.Writer("all.pdb") as pdb:
As simple as that! Took me a little while to find out.
If you have multiple frames you can write in the
with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb:
for _ in universe.trajectory: