[gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp

[Mark Abraham]

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