Improvements to GROMACS tools¶
gmx pdb2gmx now resolves generated hydrogen names from the residue topology¶
When gmx pdb2gmx adds hydrogens from the hydrogen database, it now looks up
their names in the residue topology entry of the selected force field instead of
relying on hard-coded numbering rules. This allows force fields that use
different hydrogen naming schemes, such as original AMBER/IUPAC names for
methylene hydrogens, to work without naming-specific code paths or command-line
options.
-w now displays more file types, and falls back to other viewers¶
The -w option can now display .cif and .gro files, neither of which
had a viewer before. Every file type it handles now lists several viewers rather
than one: the viewer used previously is still preferred, and an alternative is
chosen only when that one is not installed, so -w now works on machines where
it used to fail. Structures are shown with PyMOL, ChimeraX, Jmol or VMD, plots
with Grace, and images and PostScript with the common desktop viewers. The
GMX_VIEW_ environment variables continue to override the choice.