Stefano Meliga wrote:
Protonate does the job of adding all of the hydrogens but non-polar
hydrogens are not recognised by pdb2gmx so that the topology file isn't
created.
Thus you've discovered that pdb2gmx isn't magic. It can only create
topologies whose building blocks are already defined in the so-called
residue topology files (.rtp extensions). You may need to create entries
for these. Search the wiki and chapter 5 of the manual. Depending on
your need, you may be better off using some alternative
topology-generating software.
Apparently grompp needs the *.top file in input (It says "Input/Output
error upon giving only the *.gro file in input).
grompp pre-processes a topology (.top file) in the context of a set of
simulation parameters (.mdp file) and a given starting configuration
(.gro file) to produce a run input file (.tpr). All these three input
elements are necessary; others are optional.
Does this mean that I can't run an MD simulation with a molecule with
non-polar hydrogens.
You can run one, but you need to generate a .top file first.
Mark
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